Multiple mechanisms drive genomic adaptation to extreme O(2) levels in Drosophila melanogaster.

Affiliation

Iranmehr A(#)(1), Stobdan T(#)(2), Zhou D(#)(3), Zhao H(2), Kryazhimskiy S(4), Bafna V(5), Haddad GG(6)(7)(8).
Author information:
(1)Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, CA, USA.
(2)Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
(3)Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA. [Email]
(4)Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
(5)Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA. [Email]
(6)Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA. [Email]
(7)Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA. [Email]
(8)Rady Children's Hospital, San Diego, CA, USA. [Email]
(#)Contributed equally

Abstract

To detect the genomic mechanisms underlying evolutionary dynamics of adaptation in sexually reproducing organisms, we analyze multigenerational whole genome sequences of Drosophila melanogaster adapting to extreme O2 conditions over an experiment conducted for nearly two decades. We develop methods to analyze time-series genomics data and predict adaptive mechanisms. Here, we report a remarkable level of synchronicity in both hard and soft selective sweeps in replicate populations as well as the arrival of favorable de novo mutations that constitute a few asynchronized sweeps. We additionally make direct experimental observations of rare recombination events that combine multiple alleles on to a single, better-adapted haplotype. Based on the analyses of the genes in genomic intervals, we provide a deeper insight into the mechanisms of genome adaptation that allow complex organisms to survive harsh environments.