The rat MIS1/Pvt-1 locus is syntenic with MYC on chromosome 7

Mouse Pvt-1 and rat MIS1 are frequent proviral integration sites in retrovirally induced lymphomas. The Pvt-1 locus is also involved in mouse plasmacytoma (6;15) and in the variant Burkitt lymphoma (2;8) translocations. We show that the Pvt-1/MIS1 locus is syntenic with MYC on rat chromosome 7. This is consistent with a postulate of close linkage and, possibly, a functional relationship between the MYC protooncogene and the MIS1/Pvt-1 locus.     

Genomic analyses reveal natural selection on reproduction related genes between two closely related Populus (Salicaceae) species

Identifying the factors that cause reproductive isolation and their relative importance in species divergence is crucial to our understanding of speciation processes. In most species, natural selection is commonly considered to play a large role in driving speciation. Based on whole genome re-sequencing data from 27 Populus alba and 28 Populus adenopoda individuals, we explored the factors related to reproductive isolation of these two closely related species. The results showed that the two species diverged ~5–10 million years ago (Ma), when the Qinghai–Tibet Plateau reached a certain height and the inland climate of the Asian continent became arid. In highly differentiated genomic regions, the relative divergence (F_ST) and absolute divergence (d_xy) were significantly higher than the genomic background, θπ and shared polymorphisms decreased whereas fixed differences increased, which indicated that natural selection played a key role in the reproductive isolation of the two species. In addition, we found several genes that were related to reproduction that may be involved in explaining the reproductive isolation. Using phylogenetic trees resolved from haplotype data of Populus tomentosa and P. adenopoda, the maternal origin of P. tomentosa from P. adenopoda was likely to be located in Hubei and Chongqing Provinces.     

Linkage analysis and allelic imbalance in human breast cancer kindreds using microsatellite markers from the short arm of chromosome 3

Eight Icelandic breast cancer kindreds were subjected to linkage analyses with respect to 28 microsatellite loci dispersed along the short arm of chromosome 3. Breast tumors derived from these kindreds were concurrently scored for allelic imbalance with ten of the markers. Linkage to most markers could be excluded on the basis of negative LOD scores and haplotype analyses, although some moderately positive LOD scores resulted. A high frequency of imbalance in the familial tumors was seen with two of the markers in comparison with results obtained from sporadic material. The highest frequency (68%) of imbalance was detected with the marker D3S1217, which is located on 3p14.2-p14.1. Imbalance at the D3S1211 locus, which is more telomeric (3p24.2-p22), was not significantly elevated in the familial tumors. We suggest that the genetic defect responsible for breast cancer susceptibility in these families either promotes instability in the 3p14.2-p14.1 region or enhances the selective advantage of such changes.     

Adaptive population differentiation in phenology across a latitudinal gradient in European aspen (Populus tremula, L.): a comparison of neutral markers, candidate genes and phenotypic traits

A correct timing of growth cessation and dormancy induction represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees (Rehfeldt et al. 1999; Horvath et al. 2003; Howe et al. 2003). We have studied the deciduous tree European Aspen (Populus tremula) across a latitudinal gradient and compared genetic differentiation in phenology traits with molecular markers. Trees from 12 different areas covering 10 latitudinal degrees were cloned and planted in two common gardens. Several phenology traits showed strong genetic differentiation and clinal variation across the latitudinal gradient, with Q(ST) values generally exceeding 0.5. This is in stark contrast to genetic differentiation at several classes of genetic markers (18 neutral SSRs, 7 SSRs located close to phenology candidate genes and 50 SNPs from five phenology candidate genes) that all showed F(ST) values around 0.015. We thus find strong evidence for adaptive divergence in phenology traits across the latitudinal gradient. However, the strong population structure seen at the quantitative traits is not reflected in underlying candidate genes. This result fit theoretical expectations that suggest that genetic differentiation at candidate loci is better described by F(ST) at neutral loci rather than by Q(ST) at the quantitative traits themselves.     

Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome

Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F₁ hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.     

A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants

Abstract.— Partial self-fertilization is common in higher plants. Mating system variation is known to have important consequences for how genetic variation is distributed within and among populations. Selfing is known to reduce effective population size, and inbreeding species are therefore expected to have lower levels of genetic variation than comparable out crossing taxa. However, several recent empirical studies have shown that reductions in genetic diversity within populations of inbreeding species are far greater than the expected reductions based on the reduced effective population size. Two different processes have been argued to cause these patterns, selective sweeps (or hitchhiking) and background selection. Both are expected to be most effective in reducing genetic variation in regions of low recombination rates. Selfing is known to reduce the effective recombination rate, and inbreeding taxa are thus thought to be particularly vulnerable to the effects of hitchhiking or background selection. Here I propose a third explanation for the lower-than-expected levels of genetic diversity within populations of selfing species; recurrent extinctions and recolonizations of local populations, also known as metapopulation dynamics. I show that selfing in a metapopulation setting can result in large reductions in genetic diversity within populations, far greater than expected based the lower effective population size inbreeding species is expected to have. The reason for this depends on an interaction between selfing and pollen migration.     

Human interdigitating dendritic cells induce isotype switching and IL-13-dependent IgM production in CD40-activated naive B cells

Interdigitating dendritic cells (IDC) represent a mature progeny of dendritic cells (DC) in vivo and are exhibiting a strong lymphocyte stimulatory potential. Because of the restricted localization to secondary lymphoid organs where decisive cellular interactions take place in the initial events of immunity, IDC regulatory function was addressed in relation to naive B cells. In this study, we demonstrate that human tonsillar IDC induce a dual response from CD40-activated IgD+/CD38- naive B lymphocytes. IDC direct naive B cells toward either isotype switching or an IL-13-dependent IgM secretion. IDC-dependent proliferation, isotype switching, and Ig production are all strictly mediated by soluble factors, suggesting that such skewing in B cell activation is the result of differential cytokine expression. Moreover, IDC-expressed IL-13 represents a novel source of a cytokine with recently established effects in Th2 induction as well as in immunological disorders resulting in allergic reactions.     

Floral sex ratios, disease and seed set in dioecious Silene dioica

1 In the dioecious, perennial herb Silene dioica , the density of pollen donors in a population is determined by overall plant density, the sex ratio and the proportion of plants infected with the anther-smut fungus Microbotryum violaceum , which results in permanent sterility of both male and female plants.
2 Pollinators ( Bombus spp.) were found to prefer male flowers and to avoid diseased flowers. This may result in an overall lower visitation frequency and increased risk for pollen limitation in populations with a low density of males or a high incidence of disease.
3 Compared with open-pollinated flowers, hand pollination resulted in a significant increase in the number of seeds produced per fruit in populations with an experimentally reduced proportion of males (25% and 50% male flowers) but not in a naturally male-dominated population (75% male flowers). Seed production per plant was increased by hand pollination only in the most female-dominated population. Because the floral sex ratio is often male-biased, resources rather than pollen availability are likely to set the upper limit for total seed production per individual in most healthy populations of S. dioica.
4 There was a negative relationship between seed set and incidence of disease across 22 populations in both years of a field study. However, there was no consistent difference between the responses of highly diseased populations (incidence 30–56%) and populations with a low disease incidence (incidence 0–8%) to hand pollination.
5 In a greenhouse experiment with cloned hand-pollinated females, the presence of spores on healthy flowers was found to reduce seed set significantly. In highly diseased populations, therefore, the frequent deposition of spores by flower visitors onto remaining healthy plants may decrease seed production below the potential level determined by resources or pollen availability.     

Variation in mutation rate and polymorphism among mitochondrial genes of Silene vulgaris

The prevailing wisdom of the plant mitochondrial genome is that it has very low substitution rates, thus it is generally assumed that nucleotide diversity within species will also be low. However, recent evidence suggests plant mitochondrial genes may harbor variable and sometimes high levels of within-species polymorphism, a result attributed to variance in the influence of selection. However, insufficient attention has been paid to the effect of among-gene variation in mutation rate on varying levels of polymorphism across loci. We measured levels of polymorphism in seven mitochondrial gene regions across a geographically wide sample of the plant Silene vulgaris to investigate whether individual mitochondrial genes accumulate polymorphisms equally. We found that genes vary significantly in polymorphism. Tests based on coalescence theory show that the genes vary significantly in their scaled mutation rate, which, in the absence of differences among genes in effective population size, suggests these genes vary in their underlying mutation rate. Further evidence that among-gene variance in polymorphism is due to variation in the underlying mutation rate comes from a significant positive relationship between the number of segregating sites and silent site divergence from an outgroup. Contrary to recent studies, we found unconvincing evidence of recombination in the mitochondrial genome, and generally confirm the standard model of plant mitochondria characterized by low substitution rates and no recombination. We also show no evidence of significant variation in the strength or direction of selection among genes; this result may be expected if there is no recombination. The present study provides some of the most thorough data on plant mitochondrial polymorphism, and provides compelling evidence for mutation rate variation among genes. The study also demonstrates the difficulty in establishing a null model of mitochondrial genome polymorphism, and thus the difficulty, in the absence of a comparative approach, in testing the assumption that low substitution rates in plant mitochondria lead to low polymorphism.