Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network
Genome-wide scans for signals of natural selection in human populations have identified a large number of candidate loci that underlie local adaptations. This is surprising given the relatively short evolutionary time since the divergence of the human population. One hypothesis that has not been for...
| Main Authors: | , , |
|---|---|
| Format: | Online |
| Language: | English |
| Published: |
Oxford University Press
2014
|
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316623/ |
| id |
pubmed-4316623 |
|---|---|
| recordtype |
oai_dc |
| spelling |
pubmed-43166232015-02-19 Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network Qian, Wei Zhou, Hang Tang, Kun Research Article Genome-wide scans for signals of natural selection in human populations have identified a large number of candidate loci that underlie local adaptations. This is surprising given the relatively short evolutionary time since the divergence of the human population. One hypothesis that has not been formally examined is whether and how the recent human evolution may have been shaped by coselection in the context of complex molecular interactome. In this study, genome-wide signals of selection were scanned in East Asians, Europeans, and Africans using 1000 Genome data, and subsequently mapped onto the protein–protein interaction (PPI) network. We found that the candidate genes of recent positive selection localized significantly closer to each other on the PPI network than expected, revealing substantial clustering of selected genes. Furthermore, gene pairs of shorter PPI network distances showed higher similarities of their recent evolutionary paths than those further apart. Last, subnetworks enriched with recent coselection signals were identified, which are substantially overrepresented in biological pathways related to signal transduction, neurogenesis, and immune function. These results provide the first genome-wide evidence for association of recent selection signals with the PPI network, shedding light on the potential mechanisms of recent coselection in the human genome. Oxford University Press 2014-12-21 /pmc/articles/PMC4316623/ /pubmed/25532814 http://dx.doi.org/10.1093/gbe/evu270 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Qian, Wei Zhou, Hang Tang, Kun |
| spellingShingle |
Qian, Wei Zhou, Hang Tang, Kun Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network |
| author_facet |
Qian, Wei Zhou, Hang Tang, Kun |
| author_sort |
Qian, Wei |
| title |
Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network |
| title_short |
Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network |
| title_full |
Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network |
| title_fullStr |
Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network |
| title_full_unstemmed |
Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network |
| title_sort |
recent coselection in human populations revealed by protein–protein interaction network |
| description |
Genome-wide scans for signals of natural selection in human populations have identified a large number of candidate loci that underlie local adaptations. This is surprising given the relatively short evolutionary time since the divergence of the human population. One hypothesis that has not been formally examined is whether and how the recent human evolution may have been shaped by coselection in the context of complex molecular interactome. In this study, genome-wide signals of selection were scanned in East Asians, Europeans, and Africans using 1000 Genome data, and subsequently mapped onto the protein–protein interaction (PPI) network. We found that the candidate genes of recent positive selection localized significantly closer to each other on the PPI network than expected, revealing substantial clustering of selected genes. Furthermore, gene pairs of shorter PPI network distances showed higher similarities of their recent evolutionary paths than those further apart. Last, subnetworks enriched with recent coselection signals were identified, which are substantially overrepresented in biological pathways related to signal transduction, neurogenesis, and immune function. These results provide the first genome-wide evidence for association of recent selection signals with the PPI network, shedding light on the potential mechanisms of recent coselection in the human genome. |
| publisher |
Oxford University Press |
| publishDate |
2014 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316623/ |
| _version_ |
1613184068567957504 |