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Search Results: 1 - 10 of 2450 matches for " Deborah Charlesworth "
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Balancing Selection and Its Effects on Sequences in Nearby Genome Regions
Deborah Charlesworth
PLOS Genetics , 2006, DOI: 10.1371/journal.pgen.0020064
Abstract: Our understanding of balancing selection is currently becoming greatly clarified by new sequence data being gathered from genes in which polymorphisms are known to be maintained by selection. The data can be interpreted in conjunction with results from population genetics models that include recombination between selected sites and nearby neutral marker variants. This understanding is making possible tests for balancing selection using molecular evolutionary approaches. Such tests do not necessarily require knowledge of the functional types of the different alleles at a locus, but such information, as well as information about the geographic distribution of alleles and markers near the genes, can potentially help towards understanding what form of balancing selection is acting, and how long alleles have been maintained.
Balancing selection and its effects on sequences in nearby genome regions.
Charlesworth Deborah
PLOS Genetics , 2006,
Abstract: Our understanding of balancing selection is currently becoming greatly clarified by new sequence data being gathered from genes in which polymorphisms are known to be maintained by selection. The data can be interpreted in conjunction with results from population genetics models that include recombination between selected sites and nearby neutral marker variants. This understanding is making possible tests for balancing selection using molecular evolutionary approaches. Such tests do not necessarily require knowledge of the functional types of the different alleles at a locus, but such information, as well as information about the geographic distribution of alleles and markers near the genes, can potentially help towards understanding what form of balancing selection is acting, and how long alleles have been maintained.
Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene
Gabriel A. B. Marais,Alan Forrest,Esther Kamau,Jos K?fer,Vincent Daubin,Deborah Charlesworth
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0021915
Abstract: In the plant genus Silene, separate sexes and sex chromosomes are believed to have evolved twice. Silene species that are wholly or largely hermaphroditic are assumed to represent the ancestral state from which dioecy evolved. This assumption is important for choice of outgroup species for inferring the genetic and chromosomal changes involved in the evolution of dioecy, but is mainly based on data from a single locus (ITS). To establish the order of events more clearly, and inform outgroup choice, we therefore carried out (i) multi-nuclear-gene phylogenetic analyses of 14 Silene species (including 7 hermaphrodite or gynodioecious species), representing species from both Silene clades with dioecious members, plus a more distantly related outgroup, and (ii) a BayesTraits character analysis of the evolution of dioecy. We confirm two origins of dioecy within this genus in agreement with recent work on comparing sex chromosomes from both clades with dioecious species. We conclude that sex chromosomes evolved after the origin of Silene and within a clade that includes only S. latifolia and its closest relatives. We estimate that sex chromosomes emerged soon after the split with the ancestor of S. viscosa, the probable closest non-dioecious S. latifolia relative among the species included in our study.
The organization and evolution of the human Y chromosome
Brian Charlesworth
Genome Biology , 2003, DOI: 10.1186/gb-2003-4-9-226
Abstract: The Y chromosome is probably the most bizarre part of the human genome, reflecting its unique status as a huge block of largely non-recombining DNA, maintained in a permanently heterozygous state, and transmitted solely through males [1]. Early in the history of genetics, it was realized that the pattern of sex-linked inheritance, seen in species with chromosomal sex determination, implies that the Y chromosome lacks most of the genes carried on its pairing partner, the X chromosome. HJ Muller inferred that the X and Y were originally homologous chromosomes, and that the Y had lost most of the genes that it once contained, in response to its lack of recombinational exchange with the X and its permanent heterozygosity [2].Later work has largely validated this inference, although the details of the evolutionary mechanisms leading to Y chromosome degeneration are now thought to differ substantially from that proposed by Muller [3,4]. It is also now known that Y chromosomes have evolved independently in many different groups of animals and plants that have sex chromosomes; the Y chromosomes of mammals share a common origin with each other, but have nothing in common with their counterparts in birds or Drosophila [1,5]. In addition, Y chromosomes tend to be unusually rich in repetitive DNA, which is contributed both by transposable elements and by tandem arrays of satellite DNA sequences, as is often the case for regions of the genome that have low frequencies of crossing over [1]. Much of the human Y chromosome consists of heterochromatin, made up entirely of such repeats (Figure 1) [6].The first complete sequence of a 23 megabase (Mb) euchromatic (non-heterochromatic) portion of a human Y chromosome, from a single male, has recently been published by David Page's group [7]. This is a considerable achievement, given the difficulties of sequencing chromosomes that are rich in repeats, as is the case even for the euchromatin of the human Y. The researchers exploited the f
On Historical Contextualisation: Some Critical Socio-Legal Reflections
Lorie Charlesworth
Crimes and Misdemeanours : Deviance and the Law in Historical Perspective , 2007,
Abstract: This article examines the relationship of historico-legal studies to the wider context of socio-legal studies. It issues a challenge to rethink the nature and role of legal history in the light of socio-legal theory and the extent to which it out to be used by legal scholars. The discussion explores the benefits to socio-legal studies of interdisciplinarity. It suggests that historical reconstructions that contextualise the law should be properly acknowledged as a subgenre at least of the socio-legal movement, not simply perceived as an add-on methodology.
Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata
Jeffrey Ross-Ibarra, Stephen I. Wright, John Paul Foxe, Akira Kawabe, Leah DeRose-Wilson, Gesseca Gos, Deborah Charlesworth, Brandon S. Gaut
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002411
Abstract: Background Many of the processes affecting genetic diversity act on local populations. However, studies of plant nucleotide diversity have largely ignored local sampling, making it difficult to infer the demographic history of populations and to assess the importance of local adaptation. Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation. Principal Findings We studied nucleotide diversity in six natural populations of Arabidopsis lyrata, using 77 loci sampled from 140 chromosomes. The six populations were highly differentiated, with a median FST of 0.52, and structure analysis revealed no evidence of admixed individuals. Average within-population diversity varied among populations, with the highest diversity found in a German population; this population harbors 3-fold higher levels of silent diversity than worldwide samples of A. thaliana. All A. lyrata populations also yielded positive values of Tajima's D. We estimated a demographic model for these populations, finding evidence of population divergence over the past 19,000 to 47,000 years involving non-equilibrium demographic events that reduced the effective size of most populations. Finally, we used the inferred demographic model to perform an initial test for local adaptation and identified several genes, including the flowering time gene FCA and a disease resistance locus, as candidates for local adaptation events. Conclusions Our results underscore the importance of population-specific, non-equilibrium demographic processes in patterning diversity within A. lyrata. Moreover, our extensive dataset provides an important resource for future molecular population genetic studies of local adaptation in A. lyrata.
A Gradual Process of Recombination Restriction in the Evolutionary History of the Sex Chromosomes in Dioecious Plants
Michael Nicolas,Gabriel Marais,Vladka Hykelova,Bohuslav Janousek,Valérie Laporte,Boris Vyskot,Dominique Mouchiroud,Ioan Negrutiu,Deborah Charlesworth,Fran?oise Monéger
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0030004
Abstract: To help understand the evolution of suppressed recombination between sex chromosomes, and its consequences for evolution of the sequences of Y-linked genes, we have studied four X-Y gene pairs, including one gene not previously characterized, in plants in a group of closely related dioecious species of Silene which have an X-Y sex-determining system (S. latifolia, S. dioica, and S. diclinis). We used the X-linked copies to build a genetic map of the X chromosomes, with a marker in the pseudoautosomal region (PAR) to orient the map. The map covers a large part of the X chromosomes—at least 50 centimorgans. Except for a recent rearrangement in S. dioica, the gene order is the same in the X chromosomes of all three species. Silent site divergence between the DNA sequences of the X and Y copies of the different genes increases with the genes' distances from the PAR, suggesting progressive restriction of recombination between the X and Y chromosomes. This was confirmed by phylogenetic analyses of the four genes, which also revealed that the least-diverged X-Y pair could have ceased recombining independently in the dioecious species after their split. Analysis of amino acid replacements vs. synonymous changes showed that, with one possible exception, the Y-linked copies appear to be functional in all three species, but there are nevertheless some signs of degenerative processes affecting the genes that have been Y-linked for the longest times. Although the X-Y system evolved quite recently in Silene (less than 10 million years ago) compared to mammals (about 320 million years ago), our results suggest that similar processes have been at work in the evolution of sex chromosomes in plants and mammals, and shed some light on the molecular mechanisms suppressing recombination between X and Y chromosomes.
Towards a complete sequence of the human Y chromosome
Doris Bachtrog, Brian Charlesworth
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-5-reviews1016
Abstract: In humans, sex is determined by the presence or absence of the Y chromosome, which encodes the SRY gene necessary for testis development [1]. The Y chromosome is very unusual: it harbors just a few dozen genes, does not recombine over most of its length, is largely heterochromatic, and is riddled with repetitive DNA. Of all human chromosomes, the Y is probably the most intractable to genetic and molecular analysis; because it does not recombine during meiosis, classical linkage mapping is impossible, and the high density of repeated sequences makes physical mapping and sequencing difficult. In a recent article [2], David Page and colleagues describe the first detailed map of the non-recombining region of the human Y chromosome, providing a foundation for the sequencing and further analysis of this chromosome.The human Y chromosome is small and mostly devoid of genes, while the X chromosome, its meiotic pairing partner, contains several thousand genes [3]. Comparative studies strongly suggest that the X and Y chromosomes in mammals are descended from a homologous pair of autosomes [3,4,5]; this hypothesis is further supported by the existence of regions of homology between the two sex chromosomes [6].But how did the X and Y chromosomes evolve to become so different? A likely scenario is that the pair of autosomes that would eventually become the sex chromosomes acquired a sex-determining role, and suppression of recombination between the nascent Y and X chromosomes allowed them to evolve independently [5]. The X chromosome can still recombine in females, where two X chromosomes can pair, while most of the Y chromosome is completely sheltered from crossing over. The lack of recombination over most of the Y chromosome means that natural selection is less effective in preventing the accumulation of deleterious mutations and in driving the fixation of beneficial ones, resulting in the genetic erosion of the Y chromosome [5]. In response, dosage compensation evolves to re
Density-independent population projection trajectories of chromosome-substituted lines resistant and susceptible to organophosphate insecticides in Drosophila melanogaster
Takahiro Miyo, Brian Charlesworth
BMC Genetics , 2004, DOI: 10.1186/1471-2156-5-31
Abstract: Density-independent population projection trajectories, expressed as the ratios of the number of each chromosome-substituted line to that of line SSS, for which all chromosomes were derived from the susceptible line, showed significant declines in numbers with time for all the resistant chromosome-substituted lines.The declining tendency in the density-independent population projection trajectories of the resistant chromosome-substituted lines could explain the simultaneous decline in the levels of resistance to the three organophosphates, observed in the Katsunuma population in the fall.The development of insecticide resistance in insect pest populations is a population genetic process, in which insecticides select for initially rare resistant mutants within a population [1]. Although the development of insecticide resistance is an inevitable consequence of insecticide application, because the purpose of insecticide usage is to kill a certain portion of the insect pest population, insect populations that have developed resistance to insecticides sometimes exhibit reduction in levels of resistance to insecticides, after having been released from insecticide application. The cause of this reduction in resistance levels has been controversial [2]. Crow [1] said"Since the genes causing insecticide resistance were at low frequency in the population before the insecticide began to be applied, it must ordinarily be true that they are to some extent disadvantageous; otherwise they would have been common. Therefore the selection for resistance should ordinarily involve the replacement of the original genes with R factors that, in every respect except insecticide resistance, are deleterious from a survival standpoint."Under this theory, it could be expected that there is variation in fitness among resistant and susceptible genotypes, and that resistant genotypes have lower fitness than susceptible genotypes, which could result in the change of frequencies of resistance facto
Regularity of Polynomials in Free Variables
I. Charlesworth,D. Shlyakhtenko
Mathematics , 2014,
Abstract: We show that the spectral measure of any non-commutative polynomial of a non-commutative $n$-tuple cannot have atoms if the free entropy dimension of that $n$-tuple is $n$ (see also work of Mai, Speicher, and Weber). Under stronger assumptions on the $n$-tuple, we prove that the spectral measure is not singular, and measures of intervals surrounding any point may not decay slower than polynomially as a function of the interval's length.
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