scholarly journals Natural selection interacts with the local recombination rate to shape the evolution of hybrid genomes

2017 ◽  
Author(s):  
Molly Schumer ◽  
Chenling Xu ◽  
Daniel L. Powell ◽  
Arun Durvasula ◽  
Laurits Skov ◽  
...  
Keyword(s):  
Parental Species ◽  
Fine Scale ◽  
Common Occurrence ◽  
Recombination Rates ◽  
Subsequent Evolution ◽  
Genomic Features ◽  
Local Ancestry ◽  
Swordtail Fish ◽  
Naturally Occurring ◽  
Neanderthal Admixture

AbstractWhile hybridization between species is increasingly appreciated to be a common occurrence, little is known about the forces that govern the subsequent evolution of hybrid genomes. We considered this question in three independent, naturally-occurring hybrid populations formed between swordtail fish species Xiphophorus birchmanni and X. malinche. To this end, we built a fine-scale genetic map and inferred patterns of local ancestry along the genomes of 690 individuals sampled from the three populations. In all three cases, we found hybrid ancestry to be more common in regions of high recombination and where there is linkage to fewer putative targets of selection. These same patterns are also apparent in a reanalysis of human-Neanderthal admixture. Our results lend support to models in which ancestry from the “minor” parental species persists only where it is rapidly uncoupled from alleles that are deleterious in hybrids, and show the retention of hybrid ancestry to be at least in part predictable from genomic features. Our analyses further indicate that in swordtail fish, the dominant source of selection on hybrids stems from deleterious combinations of epistatically-interacting alleles.One sentence summaryThe persistence of hybrid ancestry is predictable from local recombination rates, in three replicate hybrid populations as well as in humans.

scholarly journals Evidence for substantial fine-scale variation in recombination rates across the human genome

2004 ◽  
Vol 36 (7) ◽  
pp. 700-706 ◽  
Author(s):  
Dana C Crawford ◽  
Tushar Bhangale ◽  
Na Li ◽  
Garrett Hellenthal ◽  
Mark J Rieder ◽  
...  
Keyword(s):  
Human Genome ◽  
Fine Scale ◽  
Recombination Rates ◽  
Scale Variation

scholarly journals Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)

2019 ◽  
Vol 10 (1) ◽  
pp. 299-309 ◽  
Author(s):  
Rami-Petteri Apuli ◽  
Carolina Bernhardsson ◽  
Bastian Schiffthaler ◽  
Kathryn M. Robinson ◽  
Stefan Jansson ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Map ◽  
Recombination Rate ◽  
Gene Density ◽  
Populus Tremula ◽  
Rate Variation ◽  
Recombination Rates ◽  
Genomic Features ◽  
European Aspen ◽  
Recombination Rate Variation

The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.

Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

Nature ◽  
1992 ◽  
Vol 356 (6369) ◽  
pp. 519-520 ◽  
Author(s):  
David J. Begun ◽  
Charles F. Aquadro
Keyword(s):  
Dna Polymorphism ◽  
Recombination Rates ◽  
Naturally Occurring

scholarly journals Naturally occurring hybrids of coral reef butterflyfishes have similar fitness compared to parental species

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0173212 ◽  
Author(s):  
Stefano R. Montanari ◽  
Jean-Paul A. Hobbs ◽  
Morgan S. Pratchett ◽  
Line K. Bay ◽  
Lynne van Herwerden
Keyword(s):  
Coral Reef ◽  
Parental Species ◽  
Naturally Occurring

scholarly journals Studies in the Biochemistry of Micro-organisms. Part IX.—On the production of Mannitol from glucose by species of Aspergillus

1931 ◽  
Vol 220 (468-473) ◽  
pp. 153-171 ◽  
Keyword(s):  
Common Occurrence ◽  
Bacterial Fermentation ◽  
Naturally Occurring ◽  
Micro Organisms

Mannitol (C 6 H 14 O 6 ) is the most common of the naturally occurring hexahydric alcohols. It is a curious fact that while glucose is the most commonly occurring hexose, the corresponding alcohol, sorbitol, is of relatively uncommon occurrence, while mannose and fructose, which are structurally related to mannitol, are not of such common occurrence as glucose. Mannitol is a common constituent of many plants, but occurs principally in the curious plant exudation known as “ manna,” and is at present produced technically by two methods, both of which are open to obvious disadvantages. (a) From “manna” (b) By the bacterial fermentation of fructose.

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.

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