scholarly journals Estimating the rates of crossover and gene conversion from individual genomes

2021 ◽  
Author(s):  
Derek Setter ◽  
Sam Ebdon ◽  
Ben Jackson ◽  
Konrad Lohse
Keyword(s):  
Linkage Disequilibrium ◽  
Simple Model ◽  
Gene Conversion ◽  
House Mouse ◽  
Mus Musculus ◽  
Population Genetic ◽  
Composite Likelihood ◽  
Or Gene ◽  
Evolutionary Consequences ◽  
Dependent Probability

Recombination can occur either as a result of crossover or gene conversion events. Population genetic methods for inferring the rate of recombination from patterns of linkage disequilibrium generally assume a simple model of recombination that only involves crossover events and ignore gene conversion. However, distinguishing the two processes is not only necessary for a complete description of recombination, but also essential for understanding the evolutionary consequences of inversions and other genomic partitions in which crossover (but not gene conversion) is reduced. We present heRho, a simple composite likelihood scheme for co-estimating the rate of crossover and gene conversion from individual diploid genomes. The method is based on analytic results for the distance-dependent probability of heterozygous and homozygous states at two loci. We apply heRho to simulations and data from the house mouse Mus musculus castaneus, a well studied model. Our analyses show i) that the rates of crossover and gene conversion can be accurately co-estimated at the level of individual chromosomes and ii) that previous estimates of the population scaled rate of recombination ρ = 4Ner under a pure crossover model are likely biased

scholarly journals Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)

2019 ◽  
Author(s):  
Claire Stragier ◽  
Sylvain Piry ◽  
Anne Loiseau ◽  
Mamadou Kane ◽  
Aliou Sow ◽  
...  
Keyword(s):  
Genetic Structure ◽  
House Mouse ◽  
Population Genetic Structure ◽  
Mus Musculus ◽  
Population Genetic ◽  
Management Strategies ◽  
Mus Musculus Domesticus ◽  
Model Free ◽  
Genetic Patterns ◽  
Commensal Rodents

AbstractPopulation genetic approaches may be used to investigate dispersal patterns of species living in highly urbanized environment in order to improve management strategies for biodiversity conservation or pest control. However, in such environment, population genetic structure may reflect both current features of the cityscape and urbanization history. This can be especially relevant when focusing on exotic commensal rodents that have been introduced in numerous primary colonial European settlements. Accounting for spatial and temporal cityscape heterogeneity to determine how past and recent demographic events may interplay to shape current population genetic structure of synanthropic rodents may provide useful insights to manage their populations. In this study, we addressed these issues by focusing on the house mouse, Mus musculus domesticus, in Dakar, Senegal, where the species may have been introduced as soon as Europeans settled in the middle of the nineteenth century. We examined genetic variation at one mitochondrial locus and 15 nuclear microsatellite markers from individuals sampled in 14 sampling sites representing different stages of urbanization history and different socio-economic environments in Dakar. We used various approaches, including model-based genetic clustering and model-free smoothing of pairwise genetic estimates. We further linked observed spatial genetic patterns to historical and current features of Dakar cityscape using random forest and Bayesian conditional autoregressive models. Results are consistent with an introduction of the house mouse at colonial time and the current genetic structure exhibits a gradient-like pattern reflecting the historical process of spatially continuous expansion of the city from the first European settlement. The genetic patterns further suggest that population dynamics of the house mouse is also driven by the spatial heterogeneity of the current cityscape, including socio-economics features, that translate in habitat quality. Our results highlight the potential importance of accounting for past demographic events to understand spatial genetic patterns of nonnative invasive commensal rodents in highly urbanized environment.

scholarly journals Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1269-1278 ◽  
Author(s):  
Bernhard Haubold ◽  
Jürgen Kroymann ◽  
Andreas Ratzka ◽  
Thomas Mitchell-Olds ◽  
Thomas Wiehe
Keyword(s):  
Genetic Diversity ◽  
Arabidopsis Thaliana ◽  
Linkage Disequilibrium ◽  
Gene Conversion ◽  
Genomic Sequence ◽  
Genomic Region ◽  
Resistance To Herbivory ◽  
Linkage Disequilibria ◽  
Coalescent Simulations ◽  
The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

Early Cold Exposure: Effects on Behavioral and Physiological Thermoregulation in the House Mouse, Mus musculus

1976 ◽  
Vol 49 (2) ◽  
pp. 191-199 ◽  
Author(s):  
G. Robert Lynch ◽  
Carol Becker Lynch ◽  
Marjory Dube ◽  
Cynthia Allen
Keyword(s):  
House Mouse ◽  
Cold Exposure ◽  
Mus Musculus

scholarly journals Insights into mammalian biology from the wild house mouse Mus musculus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Megan Phifer-Rixey ◽  
Michael W Nachman
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Genetic Model ◽  
Inbred Strains ◽  
Mendelian Inheritance ◽  
Model Organisms ◽  
House Mice ◽  
Small Subset ◽  
Wild Mice ◽  
Wide Range

The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system.

Mixed sex allocation strategies in a polytocous mammal, the house mouse (Mus musculus)

2011 ◽  
Vol 65 (12) ◽  
pp. 2209-2217 ◽  
Author(s):  
Adam Dušek ◽  
Luděk Bartoš ◽  
František Sedláček
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Sex Allocation ◽  
Allocation Strategies ◽  
Polytocous Mammal

scholarly journals Epigenetic polymorphism in wild populations of Mus musculus

1963 ◽  
Vol 4 (2) ◽  
pp. 193-220 ◽  
Author(s):  
R. J. Berry
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Stabilizing Selection ◽  
British Isles ◽  
Wild Populations ◽  
Local Populations ◽  
The World ◽  
Different Populations ◽  
Different Parts

It has been suggested (Berry & Searle, 1963) that the discontinuous (‘quasi-continuous’) variants studied by Grüneberg et al. in the skeleton of rodents can be regarded as constituting epigenetic polymorphism in different populations. Comparisons have been made between the incidences of skeletal variants in house mouse populations collected from: corn ricks on a single farm in Hampshire; eleven separated localities in different parts of the British Isles; and nine other places throughout the world. These showed that the method could profitably be used for genetically characterizing and hence comparing populations. There was evidence suggestive of genetical drift between local populations and stabilizing selection over a larger area.

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