Arun Durvasula; Sriram Sankararaman (2020). "Recovering signals of ghost archaic introgression in African populations". Science Advances. 6 (7) eaax5097. Bibcode:2020SciA....6.5097D. doi:10.1126/sciadv.aax5097. PMC7015685. PMID32095519. "Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations... One interpretation of the recent time of introgression that we document is that archaic forms persisted in Africa until fairly recently. Alternately, the archaic population could have introgressed earlier into a modern human population, which then subsequently interbred with the ancestors of the populations that we have analyzed here. The models that we have explored here are not mutually exclusive, and it is plausible that the history of African populations includes genetic contributions from multiple divergent populations, as evidenced by the large effective population size associated with the introgressing archaic population... Given the uncertainty in our estimates of the time of introgression, we wondered whether jointly analyzing the CSFS from both the CEU (Utah residents with Northern and Western European ancestry) and YRI genomes could provide additional resolution. Under model C, we simulated introgression before and after the split between African and non-African populations and observed qualitative differences between the two models in the high-frequency–derived allele bins of the CSFS in African and non-African populations (fig. S40). Using ABC to jointly fit the high-frequency–derived allele bins of the CSFS in CEU and YRI (defined as greater than 50% frequency), we find that the lower limit on the 95% credible interval of the introgression time is older than the simulated split between CEU and YRI (2800 versus 2155 generations B.P.), indicating that at least part of the archaic lineages seen in the YRI are also shared with the CEU..."
Arun Durvasula; Sriram Sankararaman (2020). "Recovering signals of ghost archaic introgression in African populations". Science Advances. 6 (7) eaax5097. Bibcode:2020SciA....6.5097D. doi:10.1126/sciadv.aax5097. PMC7015685. PMID32095519. "Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations... One interpretation of the recent time of introgression that we document is that archaic forms persisted in Africa until fairly recently. Alternately, the archaic population could have introgressed earlier into a modern human population, which then subsequently interbred with the ancestors of the populations that we have analyzed here. The models that we have explored here are not mutually exclusive, and it is plausible that the history of African populations includes genetic contributions from multiple divergent populations, as evidenced by the large effective population size associated with the introgressing archaic population... Given the uncertainty in our estimates of the time of introgression, we wondered whether jointly analyzing the CSFS from both the CEU (Utah residents with Northern and Western European ancestry) and YRI genomes could provide additional resolution. Under model C, we simulated introgression before and after the split between African and non-African populations and observed qualitative differences between the two models in the high-frequency–derived allele bins of the CSFS in African and non-African populations (fig. S40). Using ABC to jointly fit the high-frequency–derived allele bins of the CSFS in CEU and YRI (defined as greater than 50% frequency), we find that the lower limit on the 95% credible interval of the introgression time is older than the simulated split between CEU and YRI (2800 versus 2155 generations B.P.), indicating that at least part of the archaic lineages seen in the YRI are also shared with the CEU..."
Bergström, A; McCarthy, S; Hui, R; Almarri, M; Ayub, Q (2020). "Insights into human genetic variation and population history from 929 diverse genomes". Science. 367 (6484) eaay5012. doi:10.1126/science.aay5012. PMC7115999. PMID32193295. "An analysis of archaic sequences in modern populations identifies ancestral genetic variation in African populations that likely predates modern humans and has been lost in most non-African populations... We found small amounts of Neanderthal ancestry in West African genomes, most likely reflecting Eurasian admixture. Despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa."
Frantz, L (2015). "Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes". Nature Genetics. 47 (10): 1141–1148. doi:10.1038/ng.3394. PMID26323058. S2CID205350534.
Gopalakrishnan, Shyam; Sinding, Mikkel-Holger S.; Ramos-Madrigal, Jazmín; Niemann, Jonas; Samaniego Castruita, Jose A.; Vieira, Filipe G.; Carøe, Christian; Montero, Marc de Manuel; Kuderna, Lukas; Serres, Aitor; González-Basallote, Víctor Manuel; Liu, Yan-Hu; Wang, Guo-Dong; Marques-Bonet, Tomas; Mirarab, Siavash; Fernandes, Carlos; Gaubert, Philippe; Koepfli, Klaus-Peter; Budd, Jane; Rueness, Eli Knispel; Heide-Jørgensen, Mads Peter; Petersen, Bent; Sicheritz-Ponten, Thomas; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, M. Thomas P. (2018). "Interspecific Gene Flow Shaped the Evolution of the Genus Canis". Current Biology. 28 (21): 3441–3449.e5. doi:10.1016/j.cub.2018.08.041. PMC6224481. PMID30344120.
Arun Durvasula; Sriram Sankararaman (2020). "Recovering signals of ghost archaic introgression in African populations". Science Advances. 6 (7) eaax5097. Bibcode:2020SciA....6.5097D. doi:10.1126/sciadv.aax5097. PMC7015685. PMID32095519. "Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations... One interpretation of the recent time of introgression that we document is that archaic forms persisted in Africa until fairly recently. Alternately, the archaic population could have introgressed earlier into a modern human population, which then subsequently interbred with the ancestors of the populations that we have analyzed here. The models that we have explored here are not mutually exclusive, and it is plausible that the history of African populations includes genetic contributions from multiple divergent populations, as evidenced by the large effective population size associated with the introgressing archaic population... Given the uncertainty in our estimates of the time of introgression, we wondered whether jointly analyzing the CSFS from both the CEU (Utah residents with Northern and Western European ancestry) and YRI genomes could provide additional resolution. Under model C, we simulated introgression before and after the split between African and non-African populations and observed qualitative differences between the two models in the high-frequency–derived allele bins of the CSFS in African and non-African populations (fig. S40). Using ABC to jointly fit the high-frequency–derived allele bins of the CSFS in CEU and YRI (defined as greater than 50% frequency), we find that the lower limit on the 95% credible interval of the introgression time is older than the simulated split between CEU and YRI (2800 versus 2155 generations B.P.), indicating that at least part of the archaic lineages seen in the YRI are also shared with the CEU..."
Bergström, A; McCarthy, S; Hui, R; Almarri, M; Ayub, Q (2020). "Insights into human genetic variation and population history from 929 diverse genomes". Science. 367 (6484) eaay5012. doi:10.1126/science.aay5012. PMC7115999. PMID32193295. "An analysis of archaic sequences in modern populations identifies ancestral genetic variation in African populations that likely predates modern humans and has been lost in most non-African populations... We found small amounts of Neanderthal ancestry in West African genomes, most likely reflecting Eurasian admixture. Despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa."
Frantz, L (2015). "Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes". Nature Genetics. 47 (10): 1141–1148. doi:10.1038/ng.3394. PMID26323058. S2CID205350534.
Gopalakrishnan, Shyam; Sinding, Mikkel-Holger S.; Ramos-Madrigal, Jazmín; Niemann, Jonas; Samaniego Castruita, Jose A.; Vieira, Filipe G.; Carøe, Christian; Montero, Marc de Manuel; Kuderna, Lukas; Serres, Aitor; González-Basallote, Víctor Manuel; Liu, Yan-Hu; Wang, Guo-Dong; Marques-Bonet, Tomas; Mirarab, Siavash; Fernandes, Carlos; Gaubert, Philippe; Koepfli, Klaus-Peter; Budd, Jane; Rueness, Eli Knispel; Heide-Jørgensen, Mads Peter; Petersen, Bent; Sicheritz-Ponten, Thomas; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, M. Thomas P. (2018). "Interspecific Gene Flow Shaped the Evolution of the Genus Canis". Current Biology. 28 (21): 3441–3449.e5. doi:10.1016/j.cub.2018.08.041. PMC6224481. PMID30344120.
Arun Durvasula; Sriram Sankararaman (2020). "Recovering signals of ghost archaic introgression in African populations". Science Advances. 6 (7) eaax5097. Bibcode:2020SciA....6.5097D. doi:10.1126/sciadv.aax5097. PMC7015685. PMID32095519. "Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations... One interpretation of the recent time of introgression that we document is that archaic forms persisted in Africa until fairly recently. Alternately, the archaic population could have introgressed earlier into a modern human population, which then subsequently interbred with the ancestors of the populations that we have analyzed here. The models that we have explored here are not mutually exclusive, and it is plausible that the history of African populations includes genetic contributions from multiple divergent populations, as evidenced by the large effective population size associated with the introgressing archaic population... Given the uncertainty in our estimates of the time of introgression, we wondered whether jointly analyzing the CSFS from both the CEU (Utah residents with Northern and Western European ancestry) and YRI genomes could provide additional resolution. Under model C, we simulated introgression before and after the split between African and non-African populations and observed qualitative differences between the two models in the high-frequency–derived allele bins of the CSFS in African and non-African populations (fig. S40). Using ABC to jointly fit the high-frequency–derived allele bins of the CSFS in CEU and YRI (defined as greater than 50% frequency), we find that the lower limit on the 95% credible interval of the introgression time is older than the simulated split between CEU and YRI (2800 versus 2155 generations B.P.), indicating that at least part of the archaic lineages seen in the YRI are also shared with the CEU..."
Bergström, A; McCarthy, S; Hui, R; Almarri, M; Ayub, Q (2020). "Insights into human genetic variation and population history from 929 diverse genomes". Science. 367 (6484) eaay5012. doi:10.1126/science.aay5012. PMC7115999. PMID32193295. "An analysis of archaic sequences in modern populations identifies ancestral genetic variation in African populations that likely predates modern humans and has been lost in most non-African populations... We found small amounts of Neanderthal ancestry in West African genomes, most likely reflecting Eurasian admixture. Despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa."
Gopalakrishnan, Shyam; Sinding, Mikkel-Holger S.; Ramos-Madrigal, Jazmín; Niemann, Jonas; Samaniego Castruita, Jose A.; Vieira, Filipe G.; Carøe, Christian; Montero, Marc de Manuel; Kuderna, Lukas; Serres, Aitor; González-Basallote, Víctor Manuel; Liu, Yan-Hu; Wang, Guo-Dong; Marques-Bonet, Tomas; Mirarab, Siavash; Fernandes, Carlos; Gaubert, Philippe; Koepfli, Klaus-Peter; Budd, Jane; Rueness, Eli Knispel; Heide-Jørgensen, Mads Peter; Petersen, Bent; Sicheritz-Ponten, Thomas; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, M. Thomas P. (2018). "Interspecific Gene Flow Shaped the Evolution of the Genus Canis". Current Biology. 28 (21): 3441–3449.e5. doi:10.1016/j.cub.2018.08.041. PMC6224481. PMID30344120.
Supplementary Materials for Recovering signals of ghost archaic introgression in African populations", section "S8.2" "We simulated data using the same priors in Section S5.2, but computed the spectrum for both YRI [West African Yoruba] and CEU [a population of European origin]. We found that the best fitting parameters were an archaic split time of 27,000 generations ago (95% HPD: 26,000-28,000), admixture fraction of 0.09 (95% HPD: 0.04-0.17), admixture time of 3,000 generations ago (95% HPD: 2,800-3,400), and an effective population size of 19,700 individuals (95% HPD: 19,300-20,200). We find that the lower bound of the admixture time is further back than the simulated split between CEU and YRI (2155 generations ago), providing some evidence in favor of a pre-Out-of-Africa event. This model suggests that many populations outside of Africa should also contain haplotypes from this introgression event, though detection is difficult because many methods use unadmixed outgroups to detect introgressed haplotypes [Browning et al., 2018, Skov et al., 2018, Durvasula and Sankararaman, 2019] (5, 53, 22). It is also possible that some of these haplotypes were lost during the Out-of-Africa bottleneck."
Frantz, L (2015). "Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes". Nature Genetics. 47 (10): 1141–1148. doi:10.1038/ng.3394. PMID26323058. S2CID205350534.
