Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana

BACKGROUND: Rates of recombination can vary among genomic regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order. In highly self-fertilizing species such as Arabidopsis thaliana, however, heterozygosity is expected to be strongly reduced and recombination will be much less effective, so that its influence on genome organization should be greatly reduced. RESULTS: Here we investigated theoretically the joint effects of recombination and self-fertilization on base composition, and tested the predictions with genomic data from the complete A. thaliana genome. We show that, in this species, both codon-usage bias and GC content do not correlate with the local rates of crossing over, in agreement with our theoretical results. CONCLUSIONS: We conclude that levels of inbreeding modulate the effect of recombination on base composition, and possibly other genomic features (for example, transposable element dynamics). We argue that inbreeding should be considered when interpreting patterns of molecular evolution

What are the sources of patient experience feedback in the UK prison setting, and what do patients and healthcare staff think about giving and receiving feedback in prison? A qualitative study

Background: The collection of patient experience feedback (PEF) has seen a marked global increase in the past decade. Research about PEF has concentrated mainly on hospital settings albeit a recent interest in primary care. There has been minimal research about PEF in the prison healthcare setting. The aim of this study was to explore the role of prison PEF, the different forms it might take and the perceptions of healthcare staff and people in prison. Methods: Qualitative face to face interview study involving 24 participants across two prisons (male and female) in the North of England, involving 12 healthcare staff and 12 patients. Framework analysis was undertaken. Results: PEF sources were variable, from informal and verbal through to formal and written. The willingness of people in prison to give PEF related to whether they felt sufficiently comfortable to raise concerns, with some feeling too frightened and having apprehension about anonymity. It was viewed as disheartening to give PEF but not be informed of any outcome. Healthcare staff opinions about PEF were divergent but they found PEF unhelpful when it was about prison regime issues rather than healthcare. Suggestions for improving the PEF process were put forward and included accessibility, anonymity and digitalisation. Conclusions: This is the first study to report findings about prison PEF. There are broad similarities between our findings and research examining hospital-based PEF. Prison healthcare services seem to be listening to patients but the ways in which PEF is collected, considered and used could be improved. Experience Framework This article is associated with the Policy & Measurement lens of The Beryl Institute Experience Framework. (https://www.theberylinstitute.org/ExperienceFramework). Access other PXJ articles related to this lens. Access other resources related to this lens

CLustre : semi-automated lineament clustering for palaeo-glacial reconstruction

Datasets containing large numbers (>10,000) of glacial lineaments are increasingly being mapped from remotely sensed data in order to develop a palaeo-glacial reconstruction or ”inversion”. The palimpsest landscape presents a complex record of past ice flow and deconstructing this information into a logical history is an involved task. One stage in this process requires the identification of sets of genetically linked lineaments that can form the basis of a reconstruction. This paper presents a semi-automated algorithm, CLustre, for lineament clustering that uses a locally adaptive, region growing, methodology. After outlining the algorithm, it is tested on synthetic datasets that simulate parallel and orthogonal cross-cutting lineaments, encompassing 1,500 separate classifications. Results show robust classification in most scenarios, although parallel overlap of lineaments can cause false positive classification unless there are differences in lineament length. Case studies for Dubawnt Lake and Victoria Island, Canada, are presented and compared to existing datasets. For Dubawnt Lake 9 out of 14 classifications directly match incorporating 89% of lineaments. For Victoria Island 57 out of 58 classifications directly match incorporating 95% of lineaments. Differences are related to small numbers of unclassified lineaments and parallel cross-cutting lineaments that are of a similar length. CLustre enables the automated, repeatable, assignment of lineaments to flow sets using defined user criteria. This is important as qualitative visual interpretation may introduce bias, potentially weakening the testability of palaeo-glacial reconstructions. In addition, once classified, summary statistics of lineament clusters can be calculated and subsequently used during the reconstruction process

Distribution of variation over populations

Understanding the significance of the distribution of genetic or phenotypic variation over populations is one of the central concerns of population genetic and ecological research. The import of the research decisively depends on the measures that are applied to assess the amount of variation residing within and between populations. Common approaches can be classified under two perspectives: differentiation and apportionment. While the former focuses on differences (distances) in trait distribution between populations, the latter considers the division of the overall trait variation among populations. Particularly when multiple populations are studied, the apportionment perspective is usually given preference (via FST/GST indices), even though the other perspective is also relevant. The differences between the two perspectives as well as their joint conceptual basis can be exposed by referring them to the association between trait states and population affiliations. It is demonstrated that the two directions, association of population affiliation with trait state and of trait state with population affiliation, reflect the differentiation and the apportionment perspective, respectively. When combining both perspectives and applying the suggested measure of association, new and efficient methods of analysis result, as is outlined for population genetic processes. In conclusion, the association approach to an analysis of the distribution of trait variation over populations resolves problems that are frequently encountered with the apportionment perspective and its commonly applied measures in both population genetics and ecology, suggesting new and more comprehensive methods of analysis that include patterns of differentiation and apportionment

Near-periodic substitution and the genetic variance induced by environmental change

We investigate a model that describes the evolution of a diploid sexual population in a changing environment. Individuals have discrete generations and are subject to selection on the phenotypic value of a quantitative trait, which is controlled by a finite number of bialleic loci. Environmental change is taken to lead to a uniformly changing optimal phenotypic value. The population continually adapts to the changing environment, by allelic substitution, at the loci controlling the trait. We investigate the detailed interrelation between the process of allelic substitution and the adaptation and variation of the population, via infinite population calculations and finite population simulations. We find a simple relation between the substitution rate and the rate of change of the optimal phenotypic value

High DNA sequence diversity in pericentromeric genes of the plant Arabidopsis lyrata

Differences in neutral diversity at different loci are predicted to arise due to differences in mutation rates and from the “hitchhiking” effects of natural selection. Consistent with hitchhiking models, Drosophila melanogaster chromosome regions with very low recombination have unusually low nucleotide diversity. We compared levels of diversity from five pericentromeric regions with regions of normal recombination in Arabidopsis lyrata, an outcrossing close relative of the highly selfing A. thaliana. In contrast with the accepted theoretical prediction, and the pattern in Drosophila, we found generally high diversity in pericentromeric genes, which is consistent with the observation in A. thaliana. Our data rule out balancing selection in the pericentromeric regions, suggesting that hitchhiking is more strongly reducing diversity in the chromosome arms than the pericentromere regions

Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species

Population genetic theory predicts that the efficacy of natural selection in a self-fertilizing species should be lower than its outcrossing relatives because of the reduction in the effective population size (Ne) in the former brought about by inbreeding. However, previous analyses comparing Arabidopsis thaliana (selfer) with A. lyrata (outcrosser) have not found conclusive support for this prediction. In this study, we addressed this issue by examining silent site polymorphisms (synonymous and intronic), which are expected to be informative about changes in Ne. Two comparisons were made: A. thaliana versus A. lyrata and Capsella rubella (selfer) versus C. grandiflora (outcrosser). Extensive polymorphism data sets were obtained by compiling published data from the literature and by sequencing 354 exon loci in C. rubella and 89 additional loci in C. grandiflora. To extract information from the data effectively for studying these questions, we extended two recently developed models in order to investigate detailed selective differences between synonymous codons, mutational biases, and biased gene conversion (BGC), taking into account the effects of recent changes in population size. We found evidence that selection on synonymous codons is significantly weaker in the selfers compared with the outcrossers and that this difference cannot be fully accounted for by mutational biases or BGC

The propagation of a cultural or biological trait by neutral genetic drift in a subdivided population

We study fixation probabilities and times as a consequence of neutral genetic drift in subdivided populations, motivated by a model of the cultural evolutionary process of language change that is described by the same mathematics as the biological process. We focus on the growth of fixation times with the number of subpopulations, and variation of fixation probabilities and times with initial distributions of mutants. A general formula for the fixation probability for arbitrary initial condition is derived by extending a duality relation between forwards- and backwards-time properties of the model from a panmictic to a subdivided population. From this we obtain new formulae, formally exact in the limit of extremely weak migration, for the mean fixation time from an arbitrary initial condition for Wright's island model, presenting two cases as examples. For more general models of population subdivision, formulae are introduced for an arbitrary number of mutants that are randomly located, and a single mutant whose position is known. These formulae contain parameters that typically have to be obtained numerically, a procedure we follow for two contrasting clustered models. These data suggest that variation of fixation time with the initial condition is slight, but depends strongly on the nature of subdivision. In particular, we demonstrate conditions under which the fixation time remains finite even in the limit of an infinite number of demes. In many cases - except this last where fixation in a finite time is seen - the time to fixation is shown to be in precise agreement with predictions from formulae for the asymptotic effective population size.Comment: 17 pages, 8 figures, requires elsart5p.cls; substantially revised and improved version; accepted for publication in Theoretical Population Biolog