scholarly journals Effect of Heterogeneity in Recombination Rate on Variation in Realised Relationship

2018 ◽  
Author(s):  
Ian M.S. White ◽  
William G. Hill
Keyword(s):  
Recombination Rate ◽  
Genetic Information ◽  
Fine Scale ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Identical By Descent ◽  
Small Influence ◽  
Scale Levels ◽  
Pedigree Relationship ◽  
Actual Relationship

ABSTRACTIndividuals of specified pedigree relationship vary in the proportion of the genome they share identical by descent, i.e. in their realised or actual relationship. Basing predictions of the variance in realised relationship solely on the proportion of the map length shared implicitly assumes that both recombination rate and genetic information are uniformly distributed along the genome, ignoring the possible existence of recombination hotspots, and failing to distinguish between coding and non-coding sequences. In this paper we quantify the effects of heterogeneity in recombination rate at broad and fine scale levels on the variation in realised relationship. A chromosome with variable recombination rate usually shows more variance in realised relationship than does one having the same map length with constant recombination rate, especially if recombination rates are higher towards chromosome ends. Reductions in variance can also be found, and the overall pattern of change is quite complex. In general, local (fine-scale) variation in recombination rate, e.g. hotspots, has a small influence on the variance in realised relationship. Differences in rates across longer regions and between chromosome ends can increase or decrease the variance in realised relationship, depending on the genomic architecture.

scholarly journals Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2213-2233 ◽  
Author(s):  
Na Li ◽  
Matthew Stephens
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Population Sample ◽  
Simulated Data ◽  
Region Of Interest ◽  
Population Data ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Recombination Hotspots ◽  
Genomic Regions

AbstractWe introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a “block-like” structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.

scholarly journals A glance at recombination hotspots in the domestic cat

2015 ◽  
Author(s):  
Hasan Alhaddad ◽  
Chi Zhang ◽  
Bruce Rannala ◽  
Leslie A Lyons
Keyword(s):  
Recombination Rate ◽  
Gc Content ◽  
Domestic Cat ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Regional Population ◽  
Variable Population ◽  
Line Elements ◽  
Population Recombination ◽  
Region Size

Recombination has essential roles in increasing genetic variability within a population and in ensuring successful meiotic events. The objective of this study is to (i) infer the population scaled recombination rate (ρ), and (ii) identify and characterize localities of increased recombination rate for the domestic cat, Felis silvestris catus. SNPs (n = 701) were genotyped in twenty-two cats of Eastern random bred origin. The SNPs covered ten different chromosomal regions (A1, A2, B3, C2, D1, D2, D4, E2, F2, X) with an average region size of 850 Kb and an average SNP density of 70 SNPs/region. The Bayesian method in the program inferRho was used to infer regional population recombination rates and hotspots localities. The regions exhibited variable population recombination rates and four decisive recombination hotspots were identified on cat chromosome A2, D1, and E2 regions. No correlation was detected between the GC content and the locality of recombination spots. The hotspots enclosed L2 LINE elements and MIR and tRNA-Lys SINE elements in agreement with hotspots found in other mammals.

scholarly journals Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

2018 ◽  
Author(s):  
Enrique J. Schwarzkopf ◽  
Juan C. Motamayor ◽  
Omar E. Cornejo
Keyword(s):  
Genetic Differentiation ◽  
Recombination Rate ◽  
Plant Domestication ◽  
Population Divergence ◽  
Sequence Motifs ◽  
Recombination Rates ◽  
Genomic Features ◽  
Recombination Hotspots ◽  
Genomic Locations ◽  
Dna Sequence Motifs

AbstractOur study investigates the possible drivers of recombination hotspots in Theobroma cacao using ten genetically differentiated populations. By comparing recombination patterns between multiple populations, we obtain a novel view of recombination at the population-divergence timescale. For each population, a fine-scale recombination map was generated using the coalescent with a standard method based on linkage disequilibrium (LD). These maps revealed higher recombination rates in a domesticated population and a population that has undergone a recent bottleneck. We inferred hotspots of recombination for each population and find that the genomic locations of hotspots correlate with genetic differentiation between populations (FST). We used randomization approaches to generate appropriate null models to understand the association between hotspots of recombination and both DNA sequence motifs and genomic features. We found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. Our findings indicate that recombination hotspots are evolving in a way that is consistent with genetic differentiation but are also preferentially driven to near coding regions. We illustrate that, consistent with predictions in plant domestication, the recombination rate of the domesticated population is orders of magnitude higher than that of other populations. More importantly, we find two fixed mutations in the domesticated population’s FIGL1 protein. FIGL1 has been shown to increase recombination rates in Arabidopsis by several orders of magnitude, suggesting a possible mechanism for the observed increased recombination rate in the domesticated population.

scholarly journals Big data reveals fewer recombination hotspots than expected in human genome

2019 ◽  
Author(s):  
Ziqian Hao ◽  
Haipeng Li
Keyword(s):  
Artificial Intelligence ◽  
Sample Size ◽  
Recombination Rate ◽  
Genetic Maps ◽  
Recombination Activity ◽  
Recombination Rates ◽  
Accurate Identification ◽  
Data Set ◽  
Recombination Hotspots ◽  
Precise Estimation

AbstractRecombination is a major force that shapes genetic diversity. The inference accuracy of recombination rate is important and can be improved by increasing sample size. However, it has never been investigated whether sample size affects the distribution of inferred recombination activity along the genome, and the inference of recombination hotspots. In this study, we applied an artificial intelligence approach to estimate recombination rates in the UK10K human genomic data set with 7,562 genomes and in the OMNI CEU data set with 170 genomes. We found that the fluctuation of local recombination rate along the UK10K genomes is much smaller than that along the CEU genomes, and recombination activity in the UK10K genomes is also much less concentrated. The same phenomena were also observed when comparing UK10K with its two subsets with 200 and 400 genomes. In all cases, analyses of a larger number of genomes result in a more precise estimation of recombination rate and a less concentrated recombination activity with fewer recombination hotpots identified. Generally, UK10K recombination hotspots are about 2.93-14.25 times fewer than that identified in previous studies. By comparing the recombination hotspots of UK10K and its subsets, we found that the false inference of population-specific recombination hotspots could be as high as 75.86% if the number of sampled genomes is not super large. The results suggest that the uncertainty of estimated recombination rate is substantial when sample size is not super large, and more attention should be paid to accurate identification of recombination hotspots, especially population-specific recombination hotspots.Author summaryWe applied FastEPRR, an artificial intelligence method to estimate recombination rates in the UK10K data set with 7,562 genomes and established the most accurate human genetic map. By comparing with other human genetic maps, we found that analyses of a larger number of genomes result in a more precise estimation of recombination rate and a less concentrated recombination activity with fewer recombination hotpots identified. The false inference of population-specific recombination hotspots could be substantial if the number of sampled genomes is not super large.

scholarly journals Fine-scale recombination landscapes between a freshwater and marine population of threespine stickleback fish

2018 ◽  
Author(s):  
Alice F. Shanfelter ◽  
Sophie L. Archambeault ◽  
Michael A. White
Keyword(s):  
Gasterosteus Aculeatus ◽  
Demographic History ◽  
Strong Association ◽  
Threespine Stickleback ◽  
Open Chromatin ◽  
Fine Scale ◽  
Recombination Rates ◽  
Transcription Start Sites ◽  
Marine Population ◽  
Recombination Hotspots

AbstractMeiotic recombination is a highly conserved process that has profound effects on genome evolution. Recombination rates can vary drastically at a fine-scale across genomes and often localize to small recombination “hotspots” with highly elevated rates surrounded by regions with little recombination. Hotspot targeting to specific genomic locations is variable across species. In some mammals, hotspots have divergent landscapes between closely related species which is directed by the binding of the rapidly evolving protein, PRDM9. In many species outside of mammals, hotspots are generally conserved and tend to localize to regions with open chromatin such as transcription start sites. It remains unclear if the location of recombination hotspots diverge in taxa outside of mammals. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using an LD-based approach, we found recombination rates varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had divergent landscapes between stickleback populations, where only ~15% were shared, though part of this divergence could be due to demographic history. Additionally, we did not detect a strong association of PRDM9 with recombination hotspots in threespine stickleback fish. Our results suggest fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish and argue for additional molecular characterization to verify the extent of the divergence.

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 Stable recombination hotspots in birds

2015 ◽  
Author(s):  
Sonal Singhal ◽  
Ellen Leffler ◽  
Keerthi Sannareddy ◽  
Isaac Turner ◽  
Oliver Venn ◽  
...  
Keyword(s):  
Critical Role ◽  
Cpg Islands ◽  
Natural Populations ◽  
Bird Species ◽  
Indirect Evidence ◽  
Fine Scale ◽  
Recombination Rates ◽  
Transcription Start Sites ◽  
Recombination Hotspots ◽  
Meiotic Recombination Hotspots

Although the DNA-binding protein PRDM9 plays a critical role in the specification of meiotic recombination hotspots in mice and apes, it appears to be absent from many vertebrate species, including birds. To learn about the determinants of fine-scale recombination rates and their evolution in natural populations lacking PRDM9, we inferred fine-scale recombination maps from population resequencing data for two bird species, the zebra finchTaeniopygia guttata, and the long-tailed finch,Poephila acuticauda, whose divergence is on par with that between human and chimpanzee. We find that both bird species have hotspots, and these are enriched near CpG islands and transcription start sites. In sharp contrast to what is seen in mice and apes, the hotspots are largely shared between the two species, with indirect evidence of conservation extending across bird species tens of millions of years diverged. These observations link the evolution of hotspots to their genetic architecture, suggesting that in the absence of PRDM9 binding specificity, accessibility of the genome to the cellular recombination machinery, particularly around functional genomic elements, both enables increased recombination and constrains its evolution.

scholarly journals Evolutionary implications of recombination differences across diverging populations of Anopheles

2021 ◽  
Author(s):  
Joel T. Nelson ◽  
Omar E. Cornejo ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Rate Variation ◽  
Anopheles Coluzzii ◽  
Fine Scale ◽  
Recombination Rates ◽  
Population Genetic Differentiation ◽  
Recombination Hotspots

AbstractRecombination is one of the main evolutionary mechanisms responsible for changing the genomic architecture of populations; and in essence, it is the main mechanism by which novel combinations of alleles, haplotypes, are formed. A clear picture that has emerged across study systems is that recombination is highly variable, even among closely related species. However, it is only until very recently that we have started to understand how recombination variation between populations of the same species impact genetic diversity and divergence. Here, we used whole-genome sequence data to build fine-scale recombination maps for nine populations within two species of Anopheles, Anopheles gambiae and Anopheles coluzzii. The genome-wide recombination averages were on the same order of magnitude for all populations except one. Yet, we identified significant differences in fine-scale recombination rates among all population comparisons. We report that effective population sizes, and presence of a chromosomal inversion has major contribution to recombination rate variation along the genome and across populations. We identified over 400 highly variable recombination hotspots across all populations, where only 9.6% are shared between two or more populations. Additionally, our results are consistent with recombination hotspots contributing to both genetic diversity and absolute divergence (dxy) between populations and species of Anopheles. However, we also show that recombination has a small impact on population genetic differentiation as estimated with FST. The minimal impact that recombination has on genetic differentiation across populations represents the first empirical evidence against recent theoretical work suggesting that variation in recombination along the genome can mask or impair our ability to detect signatures of selection. Our findings add new understanding to how recombination rates vary within species, and how this major evolutionary mechanism can maintain and contribute to genetic variation and divergence within a prominent malaria vector.

Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9

2020 ◽  
Vol 37 (5) ◽  
pp. 1272-1294 ◽  
Author(s):  
Drew R Schield ◽  
Giulia I M Pasquesi ◽  
Blair W Perry ◽  
Richard H Adams ◽  
Zachary L Nikolakis ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Gc Content ◽  
Substantial Variation ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Functional Regions ◽  
Intergenic Regions ◽  
Positive Correlations ◽  
Adaptive Role

Abstract Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two primary models for hotspot evolution derived from mammals and birds. Species with PRDM9-directed recombination have rapid turnover of hotspots concentrated in intergenic regions (i.e., mammals), whereas hotspots in species lacking PRDM9 are concentrated in functional regions and have greater stability over time (i.e., birds). Snakes possess PRDM9, yet virtually nothing is known about snake recombination. Here, we examine the recombination landscape and test hypotheses about the roles of PRDM9 in rattlesnakes. We find substantial variation in recombination rate within and among snake chromosomes, and positive correlations between recombination rate and gene density, GC content, and genetic diversity. Like mammals, snakes appear to have a functional and active PRDM9, but rather than being directed away from genes, snake hotspots are concentrated in promoters and functional regions—a pattern previously associated only with species that lack a functional PRDM9. Snakes therefore provide a unique example of recombination landscapes in which PRDM9 is functional, yet recombination hotspots are associated with functional genic regions—a combination of features that defy existing paradigms for recombination landscapes in vertebrates. Our findings also provide evidence that high recombination rates are a shared feature of vertebrate microchromosomes. Our results challenge previous assumptions about the adaptive role of PRDM9 and highlight the diversity of recombination landscape features among vertebrate lineages.

scholarly journals Comparison of fine-scale recombination maps in fungal plant pathogens reveals dynamic recombination landscapes and intragenic hotspots

2017 ◽  
Author(s):  
Eva H. Stukenbrock ◽  
Julien Y. Dutheil
Keyword(s):  
Recombination Rate ◽  
Plant Pathogens ◽  
Population Genomics ◽  
Gene Evolution ◽  
Strong Impact ◽  
Recombination Rates ◽  
Zymoseptoria Tritici ◽  
Sequence Composition ◽  
Recombination Hotspots ◽  
Fungal Plant Pathogens

AbstractMeiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation and rates of adaptation. In many organisms recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Zymoseptoria ardabiliae. We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots co-localize between the two species, suggesting that hotspots dynamics contribute to the overall pattern of fast evolving recombination in these species.

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