TY - JOUR
T1 - Prevalence of negative frequency-dependent selection, revealed by incomplete selective sweeps in African populations of Drosophila melanogaster
AU - Kim, Yuseob
N1 - Funding Information:
This work was supported by grant (NRF-2015R1A4A1041997) from the National Research Foundation of Korea.
Publisher Copyright:
© 2018 by the The Korean Society for Biochemistry and Molecular Biology.
PY - 2018
Y1 - 2018
N2 - Positive selection on a new beneficial mutation generates a characteristic pattern of DNA sequence polymorphism when it reaches an intermediate allele frequency. On genome sequences of African Drosophila melanogaster, we detected such signatures of selection at 37 candidate loci and identified "sweeping haplotypes (SHs)" that are increasing or have increased rapidly in frequency due to hitchhiking. Based on geographic distribution of SH frequencies, we could infer whether selective sweeps occurred starting from de novo beneficial mutants under simple constant selective pressure. Single SHs were identified at more than half of loci. However, at many other loci, we observed multiple independent SHs, implying soft selective sweeps due to a high beneficial mutation rate or parallel evolution across space. Interestingly, SH frequencies were intermediate across multiple populations at about a quarter of the loci despite relatively low migration rates inferred between African populations. This invokes a certain form of frequency-dependent selection such as heterozygote advantage. At one locus, we observed a complex pattern of multiple independent that was compatible with recurrent frequency-dependent positive selection on new variants. In conclusion, genomic patterns of positive selection are very diverse, with equal contributions of hard and soft sweeps and a surprisingly large proportion of frequencydependent selection in D. melanogaster populations.
AB - Positive selection on a new beneficial mutation generates a characteristic pattern of DNA sequence polymorphism when it reaches an intermediate allele frequency. On genome sequences of African Drosophila melanogaster, we detected such signatures of selection at 37 candidate loci and identified "sweeping haplotypes (SHs)" that are increasing or have increased rapidly in frequency due to hitchhiking. Based on geographic distribution of SH frequencies, we could infer whether selective sweeps occurred starting from de novo beneficial mutants under simple constant selective pressure. Single SHs were identified at more than half of loci. However, at many other loci, we observed multiple independent SHs, implying soft selective sweeps due to a high beneficial mutation rate or parallel evolution across space. Interestingly, SH frequencies were intermediate across multiple populations at about a quarter of the loci despite relatively low migration rates inferred between African populations. This invokes a certain form of frequency-dependent selection such as heterozygote advantage. At one locus, we observed a complex pattern of multiple independent that was compatible with recurrent frequency-dependent positive selection on new variants. In conclusion, genomic patterns of positive selection are very diverse, with equal contributions of hard and soft sweeps and a surprisingly large proportion of frequencydependent selection in D. melanogaster populations.
KW - Drosophila
KW - Evolution
KW - Positive selection
KW - Selective sweep
UR - http://www.scopus.com/inward/record.url?scp=85042031324&partnerID=8YFLogxK
U2 - 10.5483/BMBRep.2018.51.1.226
DO - 10.5483/BMBRep.2018.51.1.226
M3 - Article
C2 - 29187282
AN - SCOPUS:85042031324
SN - 1976-6696
VL - 51
SP - 1
EP - 2
JO - BMB Reports
JF - BMB Reports
IS - 1
ER -