Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral

Abstract

Background: Adaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype. Results: We used ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments. We applied the method to noncoding Human Accelerated Elements as well as open chromatin elements previously identified in 125 human tissues and cell lines to demonstrate its utility. Then, we evaluated the impact of query region length, proxy neutral sequence length, and branch count on test sensitivity and specificity. We found that the length of the query alignment can vary between 150 bp and 1 kb without affecting the estimation of selection, while for the reference alignment, we found that a length of 3 kb is adequate for proper testing. We also simulated sequence alignments under different classes of evolution and validated our ability to distinguish positive selection from relaxation of constraint and neutral evolution. Finally, we reconfirmed that a quarter of all non-coding Human Accelerated Elements are evolving by positive selection. Conclusion: Here, we introduce a method we called adaptiPhy, which adds significant improvements to our earlier method that tests for branch-specific directional selection in noncoding sequences. The motivation for these improvements is to provide a more sensitive and better targeted characterization of directional selection and neutral evolution across the genome.

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

“…Here, we searched for regions of possible positive selection within the genomes of six coronavirus species, including SARS-CoV and SARS-CoV-2. The method we used tests for an excess of branch-specific nucleotide substitutions within a defined window relative to a neutral expectation for divergence in that window and without regard to the genetic code (Wong & Nielsen, 2004; Haygood et al, 2007; Berrio, Haygood & Wray, 2020).…”

“…Here we utilize a test for positive selection that identifies an excess of nucleotide substitutions within a defined window in the genome relative to neutral expectation using a likelihood ratio framework (Wong & Nielsen, 2004; Haygood et al, 2007). We implemented this test using adaptiPhy (Berrio, Haygood & Wray, 2020) to infer regions of the genome that were likely targets of branch-specific positive selection in several Sarbecovirus species from bat, pangolin, and human hosts. Our results recapitulate results from dN/dS-based tests that highlight S , the gene encoding Spike protein, as a prominent target of natural selection within the SARS-CoV-2 genome (Cagliani et al, 2020; Chaw et al, 2020; Li et al, 2020a).…”

Peer Review #1 of "Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function (v0.1)"

“…A crucial feature contributing to the global spread of COVID-19 is that viral shedding starts before the onset of symptoms (He et al, 2020); in contrast, shedding began two to ten days after the onset of symptoms during the SARS epidemic of 2003 (Peiris et al, 2003;Pitzer, Leung & Lipsitch, 2007) Manuscript to be reviewed substitutions within a defined window relative to a neutral expectation for divergence in that window and without regard to the genetic code (Wong & Nielsen, 2004;Haygood et al, 2007;Berrio, Haygood & Wray, 2020).…”

“…In the alternative model, all three types of evolution are permitted (neutral evolution, negative selection, and positive selection) in the foreground of the following topology: (((((SARS_CoV_2, Bat_CoV_RaTG13), Pa_CoV_Guangdong), Pa_CoV_Guangxi_P4L), (Bat_CoV_LYRa11, SARS_CoV)), Bat_CoV_BM48). This method is highly sensitive and specific and can differentiate between positive selection and relaxation of constraint (Berrio et al 2020). AdaptiPhy requires at least 3 kb reference alignment for each species that is used as a putatively neutral proxy for computing substitution rates.…”

“…In order to test for positive selection on RNA function independent of its role in coding for amino acids, we utilized a test for positive selection, adaptiPhy (Berrio, Haygood & Wray, 2020), that identifies an excess of nucleotide substitutions within a defined window in the genome relative to neutral expectation using a likelihood ratio framework (Wong & Nielsen, 2004;Haygood et al, 2007). This test infers regions of the genome that were likely targets of branch-specific positive selection in several Sarbecovirus species from bat, pangolin, and human hosts.…”