2018
DOI: 10.1101/436618
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Evidence for strong fixation bias at 4-fold degenerate sites across genes in the great tit genome

Abstract: 3It is well established that GC content varies across the genome in many species and that 4 GC biased gene conversion, one form of meiotic recombination, is likely to contribute to this 5 heterogeneity. Bird genomes provide an extraordinary system to study the impact of GC biased 6 gene conversion owed to their specific genomic features. They are characterised by a high 7 karyotype conservation with substantial heterogeneity in chromosome sizes, with up to a dozen 8 large macrochromosomes and many smaller micr… Show more

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Cited by 2 publications
(6 citation statements)
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“…For example, GCbiased gene conversion -described as the preferential conversion of 'A' or 'T' alleles to 'G' or 'C' during recombination induced repair -has been shown to significantly affect estimates of substitution rates, in particular at synonymous sites in birds (Galtier et al 2009;Weber et al 2014;Boĺivar et al 2016;Botero-Castro et al 2017;Corcoran et al 2017;Bolívar et al 2019). However, while differences in the extent of GC biased gene conversion across genes are known, much less is known about its variation over time and incorporating such biases into large scale phylogenetic frameworks is far from trivial (Gossmann et al 2018a).…”
Section: The Effect Of Varying Effective Population Size and Life-hismentioning
confidence: 99%
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“…For example, GCbiased gene conversion -described as the preferential conversion of 'A' or 'T' alleles to 'G' or 'C' during recombination induced repair -has been shown to significantly affect estimates of substitution rates, in particular at synonymous sites in birds (Galtier et al 2009;Weber et al 2014;Boĺivar et al 2016;Botero-Castro et al 2017;Corcoran et al 2017;Bolívar et al 2019). However, while differences in the extent of GC biased gene conversion across genes are known, much less is known about its variation over time and incorporating such biases into large scale phylogenetic frameworks is far from trivial (Gossmann et al 2018a).…”
Section: The Effect Of Varying Effective Population Size and Life-hismentioning
confidence: 99%
“…Due to special features of the avian karyotype, such as a stable recombinational and mutational landscape, it seems unlikely that variation in mutation rate can contribute to the patterns observed here. However, while interchromosomal re-arrangements are rare in birds, intra-chromosomal changes are more common and could lead to sudden changes in local mutation rates (Gossmann et al 2018b). Additionally, we restricted our analysis to non-coding regions that are specific to birds, or highly divergent relative to vertebrates (Seki et al 2017).…”
Section: Non-coding Regions Associated With Beak Shape Morphology Evomentioning
confidence: 99%
“…fixed by positive selection (α) (Bolívar et al, 2018;Corcoran et al, 2017;Rousselle et al, 2019). Equally, studying gBGC in coding regions is inconvenienced by the action of natural selection also acting on those regions, forcing studies to use putatively neutral sites like third codon positions (Rousselle et al, 2019;Weber et al, 2014) and 4-fold degenerate sites (Bolívar et al, 2016;Corcoran et al, 2017;Gossmann et al, 2018) reducing the amount of data available as well as potentially being confounded by codon usage bias (Chamary and Hurst, 2005;Galtier et al, 2018;Hayes et al, 2020;Jackson et al, 2017;Kunstner et al, 2011).…”
mentioning
confidence: 99%
“…The avian system has been the model of choice for many studies addressing GC evolution and biased gene conversion (Bolívar et al, 2016(Bolívar et al, , 2018(Bolívar et al, , 2019Corcoran et al, 2017;Gossmann et al, 2018;Rousselle et al, 2019;Weber et al, 2014). The suitability of avian genomes for addressing these topics stems from their variable intra genomic recombination landscapes (Backström et al, 2010;Stapley et al, 2008;van Oers et al, 2014) and conserved recombination hotspots (Singhal et al, 2015) providing a natural experiment for addressing the role of recombination and Ne in gBGC and GC content evolution.…”
mentioning
confidence: 99%
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