WorldCat Identities

Keightley, P. (Peter)

Works: 6 works in 6 publications in 1 language and 13 library holdings
Genres: Academic theses 
Publication Timeline
Most widely held works by P Keightley
Population genetics, quantitative genetics, and animal improvement : papers in honor of William (Bill) Hill : papers of a theme issue( Book )

1 edition published in 2005 in English and held by 7 WorldCat member libraries worldwide

Evolution of sex and recombination in large, finite populations by Matthew Hartfield( )

1 edition published in 2012 in English and held by 2 WorldCat member libraries worldwide

This thesis investigates how breaking apart selection interference ('Hill-Robertson' effects) that arises between linked loci can select for higher levels of recombination. Specifically, it mainly studies how the presence of both advantageous and deleterious mutation affects selection for recombination. These evolutionary advantages are subsequently investigated with regards to sex resisting asexual invasion in a subdivided population. i) KEIGHTLEY and OTTO (2006) showed a strong advantage to recombination in breaking apart selection interference, if it acts across multiple, linked loci subject to recurrent deleterious mutation. Their model is modified to consider selection acting on recombination if a small proportion of mutations are advantageous. This leads to a greater increase in selection acting on a recombination modifier, compared to cases where only deleterious mutations are present. ii) Branching-process methods are developed to quantify how likely it is that a deleterious mutant hitchhikes with a selective sweep, and how recombination between the two loci affects this process. This is compared to the neutral hitchhiking model, to determine how levels of linked neutral diversity would differ between the two scenarios. A simple application with regards to human genetic data is provided. iii) Population subdivision can maintain costly sex, as a consequence of restricted gene flow slowing the spread of invading asexuals, which leads to an excessive accumulation of deleterious alleles. However, previous work did not quantify whether costly sex can be maintained with realistic levels of population subdivision. Simulations in this thesis show that the level of population subdivision (as measured by Fst) needed to maintain costly sex decreases with larger population size; however critical Fst values found are generally high, compared to surveys of geographicallyclose populations. The lowest levels of population subdivision that maintained sex were found if mutation is both advantageous and deleterious, and demes were arranged in a one-dimensional stepping-stone formation. iv) An analytical method is developed to calculate how long it takes an advantageous mutation (such as an invading asexual) to spread through a subdivided population. The flexibility of the methods created means that they can be applied to different types of stepping-stone populations. It is shown how to formulate the fixation time for one-dimensional and two-dimensional structures, with analytical methods showing a good fit to simulation data
Understanding variation in nucleotide diversity across the mouse genome by Thomas Rhys Booker( )

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

Next-generation nematode genomes by Sujai Kumar( )

1 edition published in 2013 in English and held by 1 WorldCat member library worldwide

The first metazoan to be sequenced was a nematode (Caenorhabditis elegans), and understanding the genome of this model organism has led to many insights about all animals. Although eleven nematode genomes have been published so far and approximately twenty more are under way, the vast majority of the genomes of this incredibly diverse phylum remain unexplored. Next-generation sequencing has made it possible to generate large amounts of genome sequence data in a few days at a fraction of the cost of traditional Sanger-sequencing. However, assembling and annotating these data into genomic resources remains a challenge because of the short reads, the quality issues in these kinds of data, and the presence of contaminants and co-bionts in uncultured samples. In this thesis, I describe the process of creating high quality draft genomes and annotation resources for four nematode species representing three of the five major nematode clades: Caenorhabditis sp. 5, Meloidogyne floridensis, Dirofilaria immitis, and Litomosoides sigmodontis. I describe the new approaches I developed for visualising contamination and co-bionts, and I present the details of the robust workflow I devised to deal with the problems of generating low-cost genomic resources from Illumina short-read sequencing. Results: The draft genome assemblies created using the workflow described in this thesis are comparable to the draft nematode genomes created using Sanger sequencing. Armed with these genomes, I was able to answer two evolutionary genomics questions at very different scales. The first question was whether any non-coding elements were deeply conserved at the level of the whole phylum. Such elements had previously been hypothesised to be responsible for the phylum body plan in vertebrates, insects, and nematodes. I used twenty nematode genomes in several whole-genome alignments and concluded that no such elements were conserved across the whole phylum. The second question addressed the origins of the highly destructive plant-parasitic root-knot nematode Meloidogyne incognita. Comparisons with the newly sequenced Meloidogyne floridensis genome revealed the complex hybrid origins of both species, undermining previous assumptions about the rarity of hybrid speciation in animals. Conclusions: This thesis demonstrates the role of next-generation sequencing in democratising genome sequencing projects. Using the sequencing strategies, workflows, and tools described here, one can rapidly create genomic resources at a very low cost, even for unculturable metazoans. These genomes can be used to understand the evolutionary history of a genus or a phylum, as shown
Fitness effects of new mutations and adaptive evolution in house mice by Athanasios Kousathanas( )

1 edition published in 2013 in English and held by 1 WorldCat member library worldwide

Inferring strength of selection in vertebrate genomes by Lél Eöry( )

1 edition published in 2011 in English and held by 1 WorldCat member library worldwide

Protein-coding sequences have long been assumed to evolve under selection, but the quantification of the process at the nucleotide sequence level only started when a simple null model, the neutral theory of molecular evolution, was formulated by Kimura. Several methods were developed, which were based on the assumption that synonymous sites (nucleotides at third codon positions which do not change the encoded amino acid) evolve close to neutrally, and could be used as local neutral standards. Most of our current knowledge on the direction and strength of selection still depends on this simple assumption. One method, notably the non-synonymous to synonymous substitution rate ratio (dN/dS) has gained prevalence and is still widely used, in spite of the growing body of evidence that synonymous sites evolve under selection. In this thesis, I quantify the strength of selection in different sequence compartments of mammalian genomes, in order to obtain estimates of their functional importance from comparative genomics analyses. I quantify the fraction of mutations that have been selectively eliminated since the divergence of the species pairs examined, the so called genome wide selective constraint. This in turn is used to approximate the genomic deleterious mutation rate, which is an important parameter for several evolutionary problems. As estimates of selection depend on a large extent on the chosen neutral standard, here I use orthologous transposable elements, so called ancestral repeats, as these have been found to be evolving at a largely neutral fashion, and contain the least number of constrained sites in mammalian genomes. This enables me to quantify the level of selection even at synonymous sites, and the results suggest that these sites indeed evolve under constraint, the consequences of which I discuss. The selective constraint estimates enable me to test some simple hypotheses, such as Ohta's nearly neutral theory of molecular evolution, which suggests that selection is more efficient in species with larger effective population sizes. Beside the choice of neutral standards, there are several additional factors which are known to affect the selective constraint estimates. Here I also test the consequences of one of these, notably when sequences are not at compositional equilibrium (i.e. their GC content is away from the equilibrium GC content), which predicts that sequences with different GC content should evolve with different rates. This can cause bias in the estimates of level of selection or can even imitate selection in sequences which evolve completely neutrally. This effect is quantified here, and a simple correction is discussed
Audience Level
Audience Level
  Kids General Special  
Audience level: 0.81 (from 0.79 for Evolution ... to 0.84 for Understand ...)

Associated Subjects
Alternative Names
Keightley, Peter

Peter Keightley British scientist

Peter Keightley científico británico

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