Models of archaic admixture and recent history from two-locus statistics.
We learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibri...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2019-06-01
|
| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1008204 |
| _version_ | 1819001981245587456 |
|---|---|
| author | Aaron P Ragsdale Simon Gravel |
| author_facet | Aaron P Ragsdale Simon Gravel |
| author_sort | Aaron P Ragsdale |
| collection | DOAJ |
| description | We learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4 - 8% genetic ancestry to individuals in world-wide populations. |
| first_indexed | 2024-12-20T22:57:50Z |
| format | Article |
| id | doaj.art-85bc6046c80b432b9e7ce2b24cfe4e05 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-20T22:57:50Z |
| publishDate | 2019-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-85bc6046c80b432b9e7ce2b24cfe4e052022-12-21T19:24:05ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042019-06-01156e100820410.1371/journal.pgen.1008204Models of archaic admixture and recent history from two-locus statistics.Aaron P RagsdaleSimon GravelWe learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4 - 8% genetic ancestry to individuals in world-wide populations.https://doi.org/10.1371/journal.pgen.1008204 |
| spellingShingle | Aaron P Ragsdale Simon Gravel Models of archaic admixture and recent history from two-locus statistics. PLoS Genetics |
| title | Models of archaic admixture and recent history from two-locus statistics. |
| title_full | Models of archaic admixture and recent history from two-locus statistics. |
| title_fullStr | Models of archaic admixture and recent history from two-locus statistics. |
| title_full_unstemmed | Models of archaic admixture and recent history from two-locus statistics. |
| title_short | Models of archaic admixture and recent history from two-locus statistics. |
| title_sort | models of archaic admixture and recent history from two locus statistics |
| url | https://doi.org/10.1371/journal.pgen.1008204 |
| work_keys_str_mv | AT aaronpragsdale modelsofarchaicadmixtureandrecenthistoryfromtwolocusstatistics AT simongravel modelsofarchaicadmixtureandrecenthistoryfromtwolocusstatistics |