scholarly journals A Coalescent Model of Recombination Hotspots

Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 407-417 ◽  
Author(s):  
Carsten Wiuf ◽  
David Posada
Keyword(s):  
Current Debate ◽  
Expected Number ◽  
Recombination Rates ◽  
Coalescent Model ◽  
Recombination Hotspots ◽  
Snp Data ◽  
Genome Wide ◽  
Experimental Findings ◽  
Historical Recombination ◽  
Block Structured

Abstract Recent experimental findings suggest that the assumption of a homogeneous recombination rate along the human genome is too naive. These findings point to block-structured recombination rates; certain regions (called hotspots) are more prone than other regions to recombination. In this report a coalescent model incorporating hotspot or block-structured recombination is developed and investigated analytically as well as by simulation. Our main results can be summarized as follows: (1) The expected number of recombination events is much lower in a model with pure hotspot recombination than in a model with pure homogeneous recombination, (2) hotspots give rise to large variation in recombination rates along the genome as well as in the number of historical recombination events, and (3) the size of a (nonrecombining) block in the hotspot model is likely to be overestimated grossly when estimated from SNP data. The results are discussed with reference to the current debate about block-structured recombination and, in addition, the results are compared to genome-wide variation in recombination rates. A number of new analytical results about the model are derived.

scholarly journals Genome-wide recombination map construction from single individuals using linked-read sequencing

2018 ◽  
Author(s):  
Andreea Dréau ◽  
Vrinda Venu ◽  
Ludmila Gaspar ◽  
Felicity C. Jones
Keyword(s):  
Low Cost ◽  
Genomic Diversity ◽  
Single Individual ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Map Construction ◽  
Genome Wide ◽  
Genomic Location ◽  
Sperm Dna ◽  
Opening Up

Meiotic recombination is a major molecular mechanism generating genomic diversity. Recombination rates vary across the genome, often involving localized crossover “hotspots” and “coldspots”. Studying the molecular basis and mechanism underlying this variation within and among individuals has been challenging due to the high cost and effort required to construct individualized genome-wide maps of recombination crossovers. In this study we introduce a new method to detect recombination crossovers across the genome from sperm DNA using Illumina sequencing of linked-read libraries produced using 10X Genomics technology. We leverage the long range information provided by the linked short reads to phase and assign haplotype states to each DNA molecule. When applied to DNA from gametes of a diploid organism, the majority of linked-read molecules can be used to faithfully reconstruct an individual’s two haplotypes present at each location in the genome. A valuable rare fraction of molecules that span meiotic crossovers between the two chromosome haplotypes can then be isolated from the broader population of nonrecombinant molecules. Our pipeline, called ReMIX, allows us to characterize the genomic location and intensity of meiotic crossovers in a single individual and faithfully detects previously described recombination hotspots discovered by studies using mapping panels in mice. With a median crossover resolution of the mouse and stickleback being 15kb and 23kb respectively, ReMIX provides a powerful, high-throughput, low-cost approach to quantify recombination variation across the genome opening up numerous opportunities to study recombination variation with high genomic resolution in multiple individuals. ReMIX source code is available at at https://github.com/adreau/ReMIX.

scholarly journals Genome-wide recombination map construction from single individuals using linked-read sequencing

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Andreea Dréau ◽  
Vrinda Venu ◽  
Elena Avdievich ◽  
Ludmila Gaspar ◽  
Felicity C. Jones
Keyword(s):  
Meiotic Recombination ◽  
Molecular Basis ◽  
Low Cost ◽  
Single Individual ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Map Construction ◽  
Genome Wide ◽  
Genomic Location ◽  
Exciting Opportunity

Abstract Meiotic recombination rates vary across the genome, often involving localized crossover hotspots and coldspots. Studying the molecular basis and mechanisms underlying this variation has been challenging due to the high cost and effort required to construct individualized genome-wide maps of recombination crossovers. Here we introduce a new method, called ReMIX, to detect crossovers from gamete DNA of a single individual using Illumina sequencing of 10X Genomics linked-read libraries. ReMIX reconstructs haplotypes and identifies the valuable rare molecules spanning crossover breakpoints, allowing quantification of the genomic location and intensity of meiotic recombination. Using a single mouse and stickleback fish, we demonstrate how ReMIX faithfully recovers recombination hotspots and landscapes that have previously been built using hundreds of offspring. ReMIX provides a high-resolution, high-throughput, and low-cost approach to quantify recombination variation across the genome, providing an exciting opportunity to study recombination among multiple individuals in diverse organisms.

scholarly journals Recombining without hotspots: A comprehensive evolutionary portrait of recombination in two closely related species of Drosophila

2015 ◽  
Author(s):  
Caiti Smukowski Heil ◽  
Chris Ellison ◽  
Matthew Dubin ◽  
Mohamed Noor
Keyword(s):  
Recombination Rate ◽  
Multiple Scales ◽  
Sequence Data ◽  
Scale Effects ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Genome Wide ◽  
Genomic Landscape ◽  
Species Specific

Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in Metazoans by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present what may be the most comprehensive portrait of recombination to date, combining contemporary recombination estimates from each of two sister species along with historic estimates of recombination using linkage-disequilibrium-based approaches derived from sequence data from both species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we replicate the pattern seen in human-chimpanzee that recombination rate is conserved at broad scales and more divergent at finer scales. We also find evidence of a species-wide recombination modifier, resulting in both a present and historic genome wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inter-species inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms.

scholarly journals Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae

2019 ◽  
Author(s):  
Renate Heinzelmann ◽  
Daniel Rigling ◽  
György Sipos ◽  
Martin Münsterkötter ◽  
Daniel Croll
Keyword(s):  
Pathogenic Fungus ◽  
Snp Markers ◽  
Rate Variation ◽  
Recombination Rates ◽  
Evolutionary Trajectory ◽  
Armillaria Ostoyae ◽  
Recombination Hotspots ◽  
Genome Wide ◽  
A Genome ◽  
Taxonomic Groups

AbstractRecombination shapes the evolutionary trajectory of populations and plays an important role in the faithful transmission of chromosomes during meiosis. Levels of sexual reproduction and recombination are important properties of host-pathogen interactions because the speed of antagonistic co-evolution depends on the ability of hosts and pathogens to generate genetic variation. However, our understanding of the importance of recombination is limited because large taxonomic groups remain poorly investigated. Here, we analyze recombination rate variation in the basidiomycete fungus Armillaria ostoyae, which is an aggressive pathogen on a broad range of conifers and other trees. We constructed a dense genetic map using 198 single basidiospore progeny from a cross. Progeny were genotyped at a genome-wide set of single nucleotide polymorphism (SNP) markers using double digest restriction site associated DNA sequencing (ddRADseq). Based on a linkage map of on 11,700 SNPs spanning 1007.5 cM, we assembled genomic scaffolds into 11 putative chromosomes of a total genome size of 56.6 Mb. We identified 1984 crossover events among all progeny and found that recombination rates were highly variable along chromosomes. Recombination hotspots tended to be in regions close to the telomeres and were more gene-poor than the genomic background. Genes in proximity to recombination hotspots were encoding on average shorter proteins and were enriched for pectin degrading enzymes. Our analyses enable more powerful population and genome-scale studies of a major tree pathogen.

scholarly journals Individual and Cross-Cultural Differences in Semantic Intuitions: New Experimental Findings

2016 ◽  
Vol 16 (3-4) ◽  
pp. 322-357 ◽  
Author(s):  
James R. Beebe ◽  
Ryan Undercoffer
Keyword(s):  
Cultural Differences ◽  
Speech Acts ◽  
Experimental Philosophy ◽  
Cross Cultural ◽  
Current Debate ◽  
Cross Cultural Differences ◽  
Anchoring Effects ◽  
Semantic Reference ◽  
Experimental Findings ◽  
Epistemic Perspective

In 2004 Edouard Machery, Ron Mallon, Shaun Nichols and Stephen Stich published what has become one of the most widely discussed papers in experimental philosophy, in which they reported that East Asian and Western participants had different intuitions about the semantic reference of proper names. A flurry of criticisms of their work has emerged, and although various replications have been performed, many critics remain unconvinced. We review the current debate over Machery et al.’s (2004) results and take note of which objections to their work have been satisfactorily answered and which ones still need to be addressed. We then report the results of studies that reveal significant cross-cultural and intra-cultural differences in semantic intuitions when we control for variables that critics allege have had a potentially distorting effect on Machery et al.’s findings. These variables include the epistemic perspective from which participants are supposed to understand the research materials, unintended anchoring effects of those materials, and pragmatic factors involved in the interpretation of speech acts within them. Our results confirm the robustness of the cross-cultural differences observed by Machery et al. and thereby strengthen the philosophical challenge they pose.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

scholarly journals Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India

2021 ◽  
pp. 104587
Author(s):  
Arnav Mehrotra ◽  
Bharat Bhushan ◽  
Karthikeyan A ◽  
Akansha Singh ◽  
Snehasmita Panda ◽  
...  
Keyword(s):  
Divergent Selection ◽  
Snp Data ◽  
Genome Wide
Sign in / Sign up

Export Citation Format

Share Document