Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on...
Main Authors: | , , , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2007-11-01
|
Series: | PLoS Biology |
Online Access: | http://europepmc.org/articles/PMC2062478?pdf=render |
id |
doaj-6b804cd42a204968b1a74d54a4da1c4d |
---|---|
record_format |
Article |
spelling |
doaj-6b804cd42a204968b1a74d54a4da1c4d2021-07-02T11:33:14ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852007-11-01511e31010.1371/journal.pbio.0050310Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.David J BegunAlisha K HollowayKristian StevensLadeana W HillierYu-Ping PohMatthew W HahnPhillip M NistaCorbin D JonesAndrew D KernColin N DeweyLior PachterEugene MyersCharles H LangleyThe population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans.http://europepmc.org/articles/PMC2062478?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
David J Begun Alisha K Holloway Kristian Stevens Ladeana W Hillier Yu-Ping Poh Matthew W Hahn Phillip M Nista Corbin D Jones Andrew D Kern Colin N Dewey Lior Pachter Eugene Myers Charles H Langley |
spellingShingle |
David J Begun Alisha K Holloway Kristian Stevens Ladeana W Hillier Yu-Ping Poh Matthew W Hahn Phillip M Nista Corbin D Jones Andrew D Kern Colin N Dewey Lior Pachter Eugene Myers Charles H Langley Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology |
author_facet |
David J Begun Alisha K Holloway Kristian Stevens Ladeana W Hillier Yu-Ping Poh Matthew W Hahn Phillip M Nista Corbin D Jones Andrew D Kern Colin N Dewey Lior Pachter Eugene Myers Charles H Langley |
author_sort |
David J Begun |
title |
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. |
title_short |
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. |
title_full |
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. |
title_fullStr |
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. |
title_full_unstemmed |
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. |
title_sort |
population genomics: whole-genome analysis of polymorphism and divergence in drosophila simulans. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Biology |
issn |
1544-9173 1545-7885 |
publishDate |
2007-11-01 |
description |
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans. |
url |
http://europepmc.org/articles/PMC2062478?pdf=render |
work_keys_str_mv |
AT davidjbegun populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT alishakholloway populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT kristianstevens populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT ladeanawhillier populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT yupingpoh populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT matthewwhahn populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT phillipmnista populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT corbindjones populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT andrewdkern populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT colinndewey populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT liorpachter populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT eugenemyers populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans AT charleshlangley populationgenomicswholegenomeanalysisofpolymorphismanddivergenceindrosophilasimulans |
_version_ |
1721330983861485568 |