scholarly journals GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Paulina Bolívar ◽  
Laurent Guéguen ◽  
Laurent Duret ◽  
Hans Ellegren ◽  
Carina F. Mugal
Genetics ◽  
1983 ◽  
Vol 105 (2) ◽  
pp. 461-468
Author(s):  
James Bruce Walsh

ABSTRACT The implications of biased gene conversion acting on selectively neutral alleles are investigated for a single diallelic locus in a finite population. Even a very slight conversion bias can significantly alter fixation probabilities. We argue that most newly arising mutants will be at a conversion disadvantage, resulting in a potentially greatly decreased substitution rate of new alleles compared with predictions from strict neutral theory. Thus, conversion bias potential allows for conservation of particular alleles without having to invoke selection. Conversely, we also show that bias can be important in the maintenance of repeated gene families without altering the substitution rate at other loci that experience the same amount of conversion bias, provided that the number of genes in the family is sufficiently large. Bias can, therefore, be important at the genomic level and yet be unimportant at the populational level. Finally, we discuss the role of biased gene conversion in speciation events, concluding that this type of molecular turnover acting independently at many individual loci is very unlikely to decrease the time required for two allopatric populations to speciate.


Author(s):  
Yichen Dai ◽  
Sonia Trigueros ◽  
Peter W. H. Holland

AbstractGerbils are a subfamily of rodents living in arid regions of Asia and Africa. Recent studies have shown that several gerbil species have unusual amino acid changes in the PDX1 protein, a homeodomain transcription factor essential for pancreatic development and β-cell function. These changes were linked to strong GC-bias in the genome that may be caused by GC-biased gene conversion, and it has been hypothesized that this caused accumulation of deleterious changes. Here we use two approaches to examine if the unusual changes are adaptive or deleterious. First, we compare PDX1 protein sequences between 38 rodents to test for association with habitat. We show the PDX1 homeodomain is almost totally conserved in rodents, apart from gerbils, regardless of habitat. Second, we use ectopic gene overexpression and gene editing in cell culture to compare functional properties of PDX1 proteins. We show that the divergent gerbil PDX1 protein inefficiently binds an insulin gene promoter and ineffectively regulates insulin expression in response to high glucose in rat cells. The protein has, however, retained the ability to regulate some other β-cell genes. We suggest that during the evolution of gerbils, the selection-blind process of biased gene conversion pushed fixation of mutations adversely affecting function of a normally conserved homeodomain protein. We argue these changes were not entirely adaptive and may be associated with metabolic disorders in gerbil species on high carbohydrate diets. This unusual pattern of molecular evolution could have had a constraining effect on habitat and diet choice in the gerbil lineage.


Gene ◽  
2010 ◽  
Vol 463 (1-2) ◽  
pp. 49-55 ◽  
Author(s):  
Yvonne Döring ◽  
Ulrich Zechner ◽  
Christian Roos ◽  
David Rosenkranz ◽  
Hans Zischler ◽  
...  

2008 ◽  
Vol 67 (4) ◽  
pp. 418-426 ◽  
Author(s):  
John J. Welch ◽  
Adam Eyre-Walker ◽  
David Waxman

2010 ◽  
Vol 24 (S1) ◽  
Author(s):  
Andrew David Bergemann ◽  
Joy S. Reidenberg ◽  
Jeffrey T. Laitman ◽  
Lucy Skrabanek ◽  
Isabel Genecin

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160463 ◽  
Author(s):  
Thibault Latrille ◽  
Laurent Duret ◽  
Nicolas Lartillot

In humans and many other species, recombination events cluster in narrow and short-lived hot spots distributed across the genome, whose location is determined by the Zn-finger protein PRDM9. To explain these fast evolutionary dynamics, an intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased gene conversion, mediated by double-strand breaks, resulting in hot-spot extinction, followed by positive selection favouring new PRDM9 alleles recognizing new sequence motifs. Thus far, however, this Red Queen model has not been formalized as a quantitative population-genetic model, fully accounting for the intricate interplay between biased gene conversion, mutation, selection, demography and genetic diversity at the PRDM9 locus. Here, we explore the population genetics of the Red Queen model of recombination. A Wright–Fisher simulator was implemented, allowing exploration of the behaviour of the model (mean equilibrium recombination rate, diversity at the PRDM9 locus or turnover rate) as a function of the parameters (effective population size, mutation and erosion rates). In a second step, analytical results based on self-consistent mean-field approximations were derived, reproducing the scaling relations observed in the simulations. Empirical fit of the model to current data from the mouse suggests both a high mutation rate at PRDM9 and strong biased gene conversion on its targets. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.


2013 ◽  
Vol 30 (7) ◽  
pp. 1700-1712 ◽  
Author(s):  
Carina F. Mugal ◽  
Peter F. Arndt ◽  
Hans Ellegren

Evolution ◽  
2013 ◽  
Vol 67 (9) ◽  
pp. 2604-2613 ◽  
Author(s):  
Evgeny V. Leushkin ◽  
Georgii A. Bazykin

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