%0 Journal Article %1 phung2016determining %A Phung, Tanya N. %A Huber, Christian D. %A Lohmueller, Kirk E. %D 2016 %I Public Library of Science %J PLOS Genetics %K CpG background_selection human_genome linked_selection %N 8 %P 1-27 %R 10.1371/journal.pgen.1006199 %T Determining the Effect of Natural Selection on Linked Neutral Divergence across Species %U https://doi.org/10.1371/journal.pgen.1006199 %V 12 %X Genetic variation at neutral sites can be reduced through linkage to nearby selected sites. This pattern has been used to show the widespread effects of natural selection at shaping patterns of genetic diversity across genomes from a variety of species. However, it is not entirely clear whether natural selection has an effect on neutral divergence between species. Here we show that putatively neutral divergence between closely related species (human and chimp) and between distantly related pairs of species (humans and mice) show signatures consistent with having been affected by linkage to selected sites. Further, our theoretical models and simulations show that natural selection indirectly affecting linked neutral sites can generate these patterns. Unless substantially more of the genome is under the direct effects of purifying selection than currently believed, our results argue that natural selection has played an important role in shaping variation in levels of putatively neutral sequence divergence across the genome. Our findings further suggest that divergence-based estimates of neutral mutation rate variation across the genome as well as certain estimators of population history may be confounded by linkage to selected sites.

@article{phung2016determining, abstract = { Genetic variation at neutral sites can be reduced through linkage to nearby selected sites. This pattern has been used to show the widespread effects of natural selection at shaping patterns of genetic diversity across genomes from a variety of species. However, it is not entirely clear whether natural selection has an effect on neutral divergence between species. Here we show that putatively neutral divergence between closely related species (human and chimp) and between distantly related pairs of species (humans and mice) show signatures consistent with having been affected by linkage to selected sites. Further, our theoretical models and simulations show that natural selection indirectly affecting linked neutral sites can generate these patterns. Unless substantially more of the genome is under the direct effects of purifying selection than currently believed, our results argue that natural selection has played an important role in shaping variation in levels of putatively neutral sequence divergence across the genome. Our findings further suggest that divergence-based estimates of neutral mutation rate variation across the genome as well as certain estimators of population history may be confounded by linkage to selected sites.}, added-at = {2018-08-23T00:06:45.000+0200}, author = {Phung, Tanya N. and Huber, Christian D. and Lohmueller, Kirk E.}, biburl = {https://www.bibsonomy.org/bibtex/21e251bf722c811d89f83214f867c533e/peter.ralph}, doi = {10.1371/journal.pgen.1006199}, interhash = {8a6d87cd25b165146ba861e39fd396c5}, intrahash = {1e251bf722c811d89f83214f867c533e}, journal = {PLOS Genetics}, keywords = {CpG background_selection human_genome linked_selection}, month = {08}, number = 8, pages = {1-27}, publisher = {Public Library of Science}, timestamp = {2018-08-23T00:06:45.000+0200}, title = {Determining the Effect of Natural Selection on Linked Neutral Divergence across Species}, url = {https://doi.org/10.1371/journal.pgen.1006199}, volume = 12, year = 2016 }