Linked selection, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence in Quercus dentata

2021 ◽  
Author(s):  
Biao‐Feng Zhou ◽  
Yong Shi ◽  
Xue‐Yan Chen ◽  
Shuai Yuan ◽  
Yi‐Ye Liang ◽  
...  
Keyword(s):  
Ecological Adaptation ◽  
Genomic Landscape ◽  
Quercus Dentata ◽  
Linked Selection

scholarly journals Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

2017 ◽  
Vol 27 (6) ◽  
pp. 1004-1015 ◽  
Author(s):  
Fan Han ◽  
Sangeet Lamichhaney ◽  
B. Rosemary Grant ◽  
Peter R. Grant ◽  
Leif Andersson ◽  
...  
Keyword(s):  
Gene Flow ◽  
Ecological Adaptation ◽  
Darwin's Finches ◽  
Darwin’S Finches ◽  
Genomic Landscape

scholarly journals Variation in recombination rate affects detection of outliers in genome scans under neutrality

2020 ◽  
Author(s):  
Tom R. Booker ◽  
Sam Yeaman ◽  
Michael C. Whitlock
Keyword(s):  
Recombination Rate ◽  
Wide Distribution ◽  
Rate Variation ◽  
Summary Statistic ◽  
Genome Scans ◽  
Coalescent Process ◽  
Genome Wide ◽  
Genomic Landscape ◽  
Recombination Rate Variation ◽  
Linked Selection

AbstractGenome scans can potentially identify genetic loci involved in evolutionary processes such as local adaptation and gene flow. Here, we show that recombination rate variation across a neutrally evolving genome gives rise to mixed sampling distributions of mean FST, a common population genetic summary statistic. In particular, we show that in regions of low recombination the distribution of estimates have more variance and a longer tail than in more highly recombining regions. Determining outliers from the genome-wide distribution without taking local recombination rate into consideration may therefore increase the frequency of false positives in low recombination regions and be overly conservative in more highly recombining ones. We perform genome-scans on simulated and empirical Drosophila melanogaster datasets and, in both cases, find patterns consistent with this neutral model. Similar patterns are observed for other summary statistics used to capture variation in the coalescent process. Linked selection, particularly background selection, is often invoked to explain heterogeneity in across the genome, but here we point out that even under neutrality, statistical artefacts can arise due to variation in recombination rate. Our results highlight a flaw in the design of genome scan studies and suggest that without estimates of local recombination rate, interpreting the genomic landscape of any summary statistic that captures variation in the coalescent process will be very difficult.

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