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Genetic Units (genetic + unit)
Selected AbstractsThe genic view of the process of speciationJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2001Chung-I Wu The unit of adaptation is usually thought to be a gene or set of interacting genes, rather than the whole genome, and this may be true of species differentiation. Defining species on the basis of reproductive isolation (RI), on the other hand, is a concept best applied to the entire genome. The biological species concept (BSC; Mayr, 1963) stresses the isolation aspect of speciation on the basis of two fundamental genetic assumptions , the number of loci underlying species differentiation is large and the whole genome behaves as a cohesive, or coadapted genetic unit. Under these tenets, the exchange of any part of the genomes between diverging groups is thought to destroy their integrity. Hence, the maintenance of each species' genome cohesiveness by isolating mechanisms has become the central concept of species. In contrast, the Darwinian view of speciation is about differential adaptation to different natural or sexual environments. RI is viewed as an important by product of differential adaptation and complete RI across the whole genome need not be considered as the most central criterion of speciation. The emphasis on natural and sexual selection thus makes the Darwinian view compatible with the modern genic concept of evolution. Genetic and molecular analyses of speciation in the last decade have yielded surprisingly strong support for the neo-Darwinian view of extensive genetic differentiation and epistasis during speciation. However, the extent falls short of what BSC requires in order to achieve whole-genome ,cohesiveness'. Empirical observations suggest that the gene is the unit of species differentiation. Significantly, the genetic architecture underlying RI, the patterns of species hybridization and the molecular signature of speciation genes all appear to support the view that RI is one of the manifestations of differential adaptation, as Darwin (1859, Chap. 8) suggested. The nature of this adaptation may be as much the result of sexual selection as natural selection. In the light of studies since its early days, BSC may now need a major revision by shifting the emphasis from isolation at the level of whole genome to differential adaptation at the genic level. With this revision, BSC would in fact be close to Darwin's original concept of speciation. [source] Genetic structure and differentiation of the Japanese extremely long-tailed chicken breed (Onagadori), associated with plumage colour variation: suggestions for its management and conservationANIMAL GENETICS, Issue 6 2009R. Tadano Summary The Onagadori is a distinguished chicken breed that is characterized by an extremely long tail in the male. In this breed, three different plumage colour varieties have been developed (black-breasted white, black-breasted red and white) in which the black-breasted white is believed to be the original colour of the Onagadori, based on historical records. To establish a conservation strategy, 176 birds were genotyped for autosomal microsatellites. Significant genetic distinctness was found between the original (black-breasted white) and two derivative varieties (FST = 0.091 and 0.093). At the same time, a Bayesian model-based clustering revealed that the majority of individuals belonging to the black-breasted red and white varieties had an extremely low proportion of the genome shared with the original type (black-breasted white). This suggests that derivative varieties were created by crossing with other breeds, with low introgression of the original-type genome. We propose that the three plumage colour varieties should be treated as separate genetic units in a conservation programme. [source] A Combinatorial Searching Method for Detecting a Set of Interacting Loci Associated with Complex TraitsANNALS OF HUMAN GENETICS, Issue 5 2006Qiuying Sha Summary Complex diseases are presumed to be the results of the interaction of several genes and environmental factors, with each gene only having a small effect on the disease. Mapping complex disease genes therefore becomes one of the greatest challenges facing geneticists. Most current approaches of association studies essentially evaluate one marker or one gene (haplotype approach) at a time. These approaches ignore the possibility that effects of multilocus functional genetic units may play a larger role than a single-locus effect in determining trait variability. In this article, we propose a Combinatorial Searching Method (CSM) to detect a set of interacting loci (may be unlinked) that predicts the complex trait. In the application of the CSM, a simple filter is used to filter all the possible locus-sets and retain the candidate locus-sets, then a new objective function based on the cross-validation and partitions of the multi-locus genotypes is proposed to evaluate the retained locus-sets. The locus-set with the largest value of the objective function is the final locus-set and a permutation procedure is performed to evaluate the overall p-value of the test for association between the final locus-set and the trait. The performance of the method is evaluated by simulation studies as well as by being applied to a real data set. The simulation studies show that the CSM has reasonable power to detect high-order interactions. When the CSM is applied to a real data set to detect the locus-set (among the 13 loci in the ACE gene) that predicts systolic blood pressure (SBP) or diastolic blood pressure (DBP), we found that a four-locus gene-gene interaction model best predicts SBP with an overall p-value = 0.033, and similarly a two-locus gene-gene interaction model best predicts DBP with an overall p-value = 0.045. [source] Multiple cryptic genetic units in Hypothenemus hampei (Coleoptera: Scolytinae): evidence from microsatellite and mitochondrial DNA sequence dataBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2010NATHALIE GAUTHIER Hypothenemus hampei is the most important insect pest of coffee and has spread to most coffee-growing countries worldwide. There have been very few studies and none have addressed the population genetics of the beetle using microsatellite markers. In the present study, 683 individuals collected from 37 locations in 18 countries worldwide were screened at nine polymorphic microsatellite loci. Sixty-five out the 683 and six additional individuals were analyzed on a 400-bp fragment of the mitochondrial cytochrome oxidase I gene. Bayesian clustering analysis and phylogenetic approaches were used to infer the genetic structure of H. hampei over the sampling that encompassed almost all its range. Microsatellite markers made it possible to achieve sufficiently significant power for the delineation of five morphocryptic evolutionary units. Supported by 27 new COI haplotypes, an unexpected considerably high level of genetic differentiation and genetic divergence was revealed between five geographically delineated clusters. Both markers and approaches showed that the clusters included specimens from (1) Ethiopia, (2) Kenya and Uganda, (3) Brazil, (4) Central America excluding Jamaica, and (5) all samples from Asia, West Africa, and Jamaica. These findings clearly suggest the existence of a ,species complex in H. hampei'. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101, 113,129. [source] Genetic structure of the endangered perennial plant Eryngium alpinum (Apiaceae) in an alpine valleyBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2008MYRIAM GAUDEUL We investigated the genetic structure of Eryngium alpinum (Apiaceae) in an Alpine valley where the plant occurs in patches of various sizes. In a conservation perspective, our goal was to determine whether the valley consists of one or several genetic units. Habitat fragmentation and previous observations of restricted pollen/seed dispersal suggested pronounced genetic structure, but gene dispersal often follows a leptokurtic distribution, which may lead to weak genetic structure. We used nine microsatellite loci and two nested sampling designs (50 × 50 m grid throughout the valley and 2 × 2 m grid in two 50 × 10 m quadrats). Within the overall valley, F -statistics and Bayesian approaches indicated high genetic homogeneity. This result might be explained by: (1) underestimation of long-distance pollen/seed dispersal by in situ experiments and (2) too recent fragmentation events to build up genetic structure. Spatial autocorrelation revealed isolation by distance on the overall valley but this pattern was much more pronounced in the 50 × 10 m quadrats sampled with a 2-m mesh. This was probably associated with limited primary seed dispersal, leading to the spatial clustering of half-sibs around maternal plants. We emphasize the interest of nested sampling designs and of combining several statistical tools. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 667,677. [source] | ||||||||||