Ghost population

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A ghost population is a population that has been inferred through using statistical techniques. [1]

Contents

Population studies

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]

Population genetics

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 Sapiens (Modern Humans) and Neanderthals between 360 kya to 1.02 mya.

Basal West Africans did not split before Neanderthals split from modern humans. [6] Even before 300,000 BP to 200,000 BP, when the ancestors of the modern San split from other modern humans, the group to split the most early from modern humans may have been Basal West Africans. [6]

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). [7] [8] [9] 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. [10]

Other animals

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. [11]

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. [12]

See also

Related Research Articles

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References

  1. 1 2 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.
  2. ↑ 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.
  3. ↑ Patterson, N (2012). "Ancient admixture in human history". Genetics. 192 (3): 1065–93. doi:10.1534/genetics.112.145037. PMC   3522152 . PMID   22960212.
  4. ↑ 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.
  5. ↑ Callaway, E (2015). ""Ghost population" hints at long-lost migration to the Americas". Nature. doi:10.1038/nature.2015.18029. S2CID   181337948.
  6. 1 2 Skoglund, Pontus; et al. (2017). "Reconstructing Prehistoric African Population Structure". Cell. 171 (1): 59–71.e21. doi:10.1016/j.cell.2017.08.049. ISSN   0092-8674. OCLC   7144495602. PMC   5679310 . PMID   28938123. S2CID   1257429.
  7. ↑ 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..."
  8. ↑ 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."
  9. ↑ 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.
  10. ↑ 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. 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."
  11. ↑ 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.
  12. ↑ 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. PMC   6224481 . PMID   30344120.
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