In 2004, it was proposed that maximum likelihood or Bayesian approaches that estimate the migration rates and population sizes using coalescent theory can use datasets which contain a population that has no data. This is referred to as a "ghost population". The manipulation allows exploration in the effects of missing populations on the estimation of population sizes and migration rates between two specific populations. The biases of the inferred population parameters depend on the magnitude of the migration rate from the unknown populations.[1] The technique for deriving ghost populations attracted criticism because ghost populations were the result of statistical models, along with their limitations.[2]
In 2012, DNA analysis and statistical techniques were used to infer that a now-extinct human population in northern Eurasia had interbred with both the ancestors of Europeans and a Siberian group that later migrated to the Americas. The group was referred to as a ghost population because they were identified by the echoes that they leave in genomes—not by bones or ancient DNA.[3] In 2013, another study found the remains of a member of this ghost group, fulfilling the earlier prediction that they had existed.[4][5]
According to a study published in 2020, there are indications that 2% to 19% (or about ≃6.6 and ≃7.0%) of the DNA of four West African populations may have come from an unknown archaic hominin which split from the ancestor of humans and Neanderthals between 360 kya to 1.02 mya. However, the study also suggests that at least part of this archaic admixture is also present in Eurasians/non-Africans, and that the admixture event or events range from 0 to 124 ka B.P, which includes the period before the Out-of-Africa migration and prior to the African/Eurasian split (thus affecting in part the common ancestors of both Africans and Eurasians/non-Africans).[6][7][8] Another recent study, which discovered substantial amounts of previously undescribed human genetic variation, also found ancestral genetic variation in Africans that predates modern humans and was lost in most non-Africans.[9]
Other animalsedit
In 2015, a study of the lineage and early migration of the domestic pig found that the best model that fitted the data included gene flow from a ghost population during the Pleistocene that is now extinct.[10]
A 2018 study suggests that the common ancestor of the wolf and the coyote may have interbred with an unknown canid related to the dhole.[11]
^ abBeerli, P (2004). "Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations". Molecular Ecology. 13 (4): 827–836. doi:10.1111/j.1365-294x.2004.02101.x. PMID 15012758. S2CID 18326408.
^Skatkin, M (2005). "Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations". Molecular Ecology. 14 (1): 67–73. doi:10.1111/j.1365-294X.2004.02393.x. PMID 15643951. S2CID 17600283.
^Patterson, N (2012). "Ancient admixture in human history". Genetics. 192 (3): 1065–93. doi:10.1534/genetics.112.145037. PMC3522152. PMID 22960212.
^Callaway, E (2015). ""Ghost population" hints at long-lost migration to the Americas". Nature. doi:10.1038/nature.2015.18029. S2CID 181337948.
^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. PMID 32095519. "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..."
^[1] 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."
^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. PMID 32193295. "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. PMID 26323058. S2CID 205350534.
^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. PMID 30344120.
February 16, 2024
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A ghost population is a population that has been inferred through using statistical techniques 1 Contents 1 Population studies 2 Population genetics 2 1 Humans 2 2 Other animals 3 See also 4 ReferencesPopulation studies editIn 2004 it was proposed that maximum likelihood or Bayesian approaches that estimate the migration rates and population sizes using coalescent theory can use datasets which contain a population that has no data This is referred to as a ghost population The manipulation allows exploration in the effects of missing populations on the estimation of population sizes and migration rates between two specific populations The biases of the inferred population parameters depend on the magnitude of the migration rate from the unknown populations 1 The technique for deriving ghost populations attracted criticism because ghost populations were the result of statistical models along with their limitations 2 Population genetics editHumans edit Further information Interbreeding between archaic and modern humans In 2012 DNA analysis and statistical techniques were used to infer that a now extinct human population in northern Eurasia had interbred with both the ancestors of Europeans and a Siberian group that later migrated to the Americas The group was referred to as a ghost population because they were identified by the echoes that they leave in genomes not by bones or ancient DNA 3 In 2013 another study found the remains of a member of this ghost group fulfilling the earlier prediction that they had existed 4 5 According to a study published in 2020 there are indications that 2 to 19 or about 6 6 and 7 0 of the DNA of four West African populations may have come from an unknown archaic hominin which split from the ancestor of humans and Neanderthals between 360 kya to 1 02 mya However the study also suggests that at least part of this archaic admixture is also present in Eurasians non Africans and that the admixture event or events range from 0 to 124 ka B P which includes the period before the Out of Africa migration and prior to the African Eurasian split thus affecting in part the common ancestors of both Africans and Eurasians non Africans 6 7 8 Another recent study which discovered substantial amounts of previously undescribed human genetic variation also found ancestral genetic variation in Africans that predates modern humans and was lost in most non Africans 9 Other animals edit In 2015 a study of the lineage and early migration of the domestic pig found that the best model that fitted the data included gene flow from a ghost population during the Pleistocene that is now extinct 10 A 2018 study suggests that the common ancestor of the wolf and the coyote may have interbred with an unknown canid related to the dhole 11 See also editGhost lineageReferences edit a b Beerli P 2004 Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations Molecular Ecology 13 4 827 836 doi 10 1111 j 1365 294x 2004 02101 x PMID 15012758 S2CID 18326408 Skatkin M 2005 Seeing ghosts the effect of unsampled populations on migration rates estimated for sampled populations Molecular Ecology 14 1 67 73 doi 10 1111 j 1365 294X 2004 02393 x PMID 15643951 S2CID 17600283 Patterson N 2012 Ancient admixture in human history Genetics 192 3 1065 93 doi 10 1534 genetics 112 145037 PMC 3522152 PMID 22960212 Raghavan M 2013 Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans Nature 505 7481 87 91 Bibcode 2014Natur 505 87R doi 10 1038 nature12736 PMC 4105016 PMID 24256729 Callaway E 2015 Ghost population hints at long lost migration to the Americas Nature doi 10 1038 nature 2015 18029 S2CID 181337948 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 PMC 7015685 PMID 32095519 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 1 Supplementary Materials forRecovering 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 Durvasula Arun Sankararaman Sriram 2020 Recovering signals of ghost archaic introgression in African populations Science Advances 6 7 eaax5097 Bibcode 2020SciA 6 5097D doi 10 1126 sciadv aax5097 PMC 7015685 PMID 32095519 S2CID 211472946 Bergstrom 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 PMC 7115999 PMID 32193295 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 PMID 26323058 S2CID 205350534 Gopalakrishnan Shyam Sinding Mikkel Holger S Ramos Madrigal Jazmin Niemann Jonas Samaniego Castruita Jose A Vieira Filipe G Caroe Christian Montero Marc de Manuel Kuderna Lukas Serres Aitor Gonzalez Basallote Victor 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 Jorgensen Mads Peter Petersen Bent Sicheritz Ponten Thomas Bachmann Lutz Wiig Oystein 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 PMC 6224481 PMID 30344120 Retrieved from https en wikipedia org w index php title Ghost population amp oldid 1184105086, wikipedia, wiki, book, books, library,
