Humans act against the natural process of breeder selection: A modern sickness for animal populations?

We present a new idea about the possible effects of human-induced mortality on different age cohorts (i.e., breeders vs. juveniles) in long-lived animals. Our hypothesis is based on Curios idea on the effect of natural selective processes on cohorts to explain age-related increases in fecundity (selection hypothesis). We believe that negative human pressure may modify such contribution to reproduction of good versus low quality phenotypes, altering the genetic structure of the population. Ecologists and environmental managers in general should be aware of how stochastic events provoked by humans may induce changes in the genetic structure of populations.     

Genetic Variability in Pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.) Estimated by Morphological Data and Amplified Fragment Length Polymorphism Markers

Data on genetic similarity among crop cultivars is of vital importance for the plant breeder. The objectives of this study were to group pepper (Capsicum annuum L.) genotypes into clusters according to their distances as estimated by morphological traits and amplified fragment length polymorphism (AFLP) markers and to assess the relationships between the two. Thirty-nine pepper genotypes obtained from different countries were grown in the greenhouse at University of the Free State, South Africa, during 2001 and 2002 in a randomized complete block design with three replications. A total of 20 different morphological traits were measured and six AFLP primer pairs were used to estimate pairwise genetic distances. Both datasets showed high genetic distances among the different genotypes, indicating high genetic diversity among them. The mean genetic distance among Ethiopian pungent elongated-fruit genotypes, was lower than that between them and the introduced ones. Morphological and AFLP distance estimations generally clustered together genotypes with similar fruit sizes. Significant, positive correlation was observed between morphological and AFLP diversity estimations. The narrow genetic basis among the Ethiopian pungent elongated-fruit cultivars suggests that the pepper breeding program of Ethiopia should focus on enriching its germplasm through local collection and introductions from other parts of the world.     

Patterns of Allozyme Variation at Two Stages of the Life History in Wild Rice <Emphasis Type="Italic">Oryza rufipogon</Emphasis> and Conservation Genetic Implications

Oryza rufipogon Griff. occurs widely in aquatic ecosystem of tropics and subtropics of monsoon Asia as well as Southern China. It is a vital gene source for rice breeding programs. Many populations of the species, unfortunately, have drastically diminished because of the disappearance of aquatic habitats as a result of human disturbance. In order to determine patterns of genetic variation at two stages of the life-cycle in the wild rice species, we investigated allozyme variation of four natural populations in China. Two southern populations have significant asexual reproduction while two other northern marginal populations show a mixed reproduction in China. At 22 allozyme loci, a significantly lower genetic diversity was observed in the ratoons than in the seeds of the two southern populations, whereas a significantly higher genetic diversity was found in the ratoons than in the seeds of the two northern marginal populations. The results suggest that the variation of reproductive system is probably associated with their patterns of genetic variation in the species. Moreover, a significantly higher genetic differentiation among populations found in the ratoons than in the seeds may stem from pollen-mediated gene flow among them. Finally, we propose suggestions for conservation management of the endangered species.     

A structural alphabet for local protein structures: improved prediction methods

Three-dimensional protein structures can be described with a library of 3D fragments that define a structural alphabet. We have previously proposed such an alphabet, composed of 16 patterns of five consecutive amino acids, called Protein Blocks (PBs). These PBs have been used to describe protein backbones and to predict local structures from protein sequences. The Q16 prediction rate reaches 40.7% with an optimization procedure. This article examines two aspects of PBs. First, we determine the effect of the enlargement of databanks on their definition. The results show that the geometrical features of the different PBs are preserved (local RMSD value equal to 0.41 A on average) and sequence-structure specificities reinforced when databanks are enlarged. Second, we improve the methods for optimizing PB predictions from sequences, revisiting the optimization procedure and exploring different local prediction strategies. Use of a statistical optimization procedure for the sequence-local structure relation improves prediction accuracy by 8% (Q16 = 48.7%). Better recognition of repetitive structures occurs without losing the prediction efficiency of the other local folds. Adding secondary structure prediction improved the accuracy of Q16 by only 1%. An entropy index (Neq), strongly related to the RMSD value of the difference between predicted PBs and true local structures, is proposed to estimate prediction quality. The Neq is linearly correlated with the Q16 prediction rate distributions, computed for a large set of proteins. An "expected" prediction rate QE16 is deduced with a mean error of 5%.     

Sequence variation in NPC1L1 and association with improved LDL-cholesterol lowering in response to ezetimibe treatment

Niemann-Pick C1-like 1 (NPC1L1) is an intestinal cholesterol transporter and the molecular target of ezetimibe, a cholesterol absorption inhibitor demonstrated to reduce LDL-cholesterol (LDL-C) both as monotherapy and when co-administered with 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors (statins). Interestingly, significant interindividual variability has been observed for rates of intestinal cholesterol absorption and LDL-C reductions at both baseline and post ezetimibe treatment. To test the hypothesis that genetic variation in NPC1L1 could influence the LDL-C response to ezetimibe, we performed extensive resequencing of the gene in 375 apparently healthy individuals and genotyped hypercholesterolemic patients from clinical trial cohorts. No association was observed between NPC1L1 single-nucleotide polymorphism and baseline cholesterol. However, significant associations to LDL-C response to treatment with ezetimibe were observed in patients treated with ezetimibe in two large clinical trials. Our data demonstrate that DNA sequence variants in NPC1L1 are associated with an improvement in response to ezetimibe pharmacotherapy and suggest that detailed analysis of genetic variability in clinical trial cohorts can lead to improved understanding of factors contributing to variable drug response.     

Selfing and inbreeding depression in seeds and seedlings of Neobalanocarpus heimii (Dipterocarpaceae)

We evaluated the degree of selfing and inbreeding depression at the seed and seedling stages of a threatened tropical canopy tree, Neobalanocarpus heimii, using microsatellite markers. Selection resulted in an overall decrease in the level of surviving selfed progeny from seeds to established seedlings, indicating inbreeding depression during seedling establishment. Mean seed mass of selfed progeny was lower than that of outcrossed progeny. Since the smaller seeds suffered a fitness disadvantage at germination in N. heimii, the reduced seed mass of selfed progeny would be one of the determinants of the observed inbreeding depression during seedling establishment. High selfing rates in some mother trees could be attributed to low local densities of reproductive individuals, thus maintenance of a sufficiently high density of mature N. heimii should facilitate regeneration and conservation of the species.     

Relationship between diet and helminths in Gallotia caesaris (Sauria: Lacertidae)

Diet and helminth fauna were analysed in Gallotia caesaris, a small lacertid lizard endemic to El Hierro (Canary Islands, Spain) in order to study the evolutionary and functional relationships between the two traits. This species is omnivorous but consumed a high proportion (82.13%) of plant matter including not only seeds but also leaves and other vegetative parts. Helminth fauna included many helminth species typical of herbivorous reptiles. Both herbivory and helminth presence were higher than expected for a lizard of its size. Comparison with other lacertids suggests that both traits result from an adaptation to insular conditions but that some "evolutionary time" to develop them is needed. Canarian Gallotia lizards, a separate lineage evolving for a long time in insularity, constitutes the most advanced lacertid group in this way. Nevertheless, results for G. caesaris indicate that helminth fauna also changes seasonally tracking variation in diet (and herbivory) throughout the year, which suggests a dynamic interaction between diet and helminth parasites.     

GENETIC VARIANCE AND COVARIANCE FOR PHYSIOLOGICAL TRAITS IN LOBELIA:ARE THERE CONSTRAINTS ON ADAPTIVE EVOLUTION?

Physiological traits that control the uptake of carbon dioxide and loss of water are key determinants of plant growth and reproduction. Variation in these traits is often correlated with environmental gradients of water, light, and nutrients, suggesting that natural selection is the primary evolutionary mechanism responsible for physiological diversification. Responses to selection, however, can be constrained by the amount of standing genetic variation for physiological traits and genetic correlations between these traits. To examine the potential for constraint on adaptive evolution, we estimated the quantitative genetic basis of physiological trait variation in one population of each of two closely related species (Lobelia siphilitica and L. cardinalis). Restricted maximum likelihood analyses of greenhouse-grown half-sib families were used to estimate genetic variances and covariances for seven traits associated with carbon and water relations. We detected significant genetic variation for all traits in L. siphilitica, suggesting that carbon-gain and water-use traits could evolve in response to natural selection in this population. In particular, narrow-sense heritabilities for photosynthetic rate (A), stomatal conductance (gs), and water-use efficiency (WUE) in our L. siphilitica population were high relative to previous studies in other species. Although there was significant narrow-sense heritability for A in L. cardinalis, we detected little genetic variation for traits associated with water use (gs and WUE), suggesting that our population of this species may be unable to adapt to drier environments. Despite being tightly linked functionally, the genetic correlation between A and gs was not strong and significant in either population. Therefore, our L. siphilitica population would not be genetically constrained from evolving high A (and thus fixing more carbon for growth and reproduction) while also decreasing gs to limit water loss. However, a significant negative genetic correlation existed between WUE and plant size in L. siphilitica, suggesting that high WUE may be negatively associated with high fecundity. In contrast, our results suggest that any constraints on the evolution of photosynthetic and stomatal traits of L. cardinalis are caused primarily by a lack of genetic variation, rather than by genetic correlations between these functionally related traits.     

A general model for detecting genetic determinants underlying longitudinal traits with unequally spaced measurements and nonstationary covariance structure

A mixture model for determining quantitative trait loci (QTL) affecting growth trajectories has been proposed in the literature. In this article, we extend this model to a more general situation in which longitudinal traits for each subject are measured at unequally spaced time intervals, different subjects have different measurement patterns, and the residual correlation within subjects is nonstationary. We derive an EM-simplex hybrid algorithm to estimate the allele frequencies, Hardy-Weinberg disequilibrium, and linkage disequilibrium between QTL in the original population and parameters contained in the growth equation and in the covariance structure. A worked example of head circumference growth in 145 children is used to validate our extended model. A simulation study is performed to examine the statistical properties of the parameter estimation obtained from this example. Finally, we discuss the implications and extensions of our model for detecting QTL that affect growth trajectories.