Población fantasma

Una población fantasma es una población que se ha inferido mediante el uso de técnicas estadísticas.^[1]

Estudios de población

En 2004, se propuso que los enfoques de máxima verosimilitud o bayesianos que estiman las tasas de migración y el tamaño de la población utilizando la teoría coalescente pueden usar conjuntos de datos que contienen una población que no tiene datos. Esto se conoce como "población fantasma". La manipulación permite explorar los efectos de las poblaciones faltantes en la estimación del tamaño de la población y las tasas de migración entre dos poblaciones específicas. Los sesgos de los parámetros poblacionales inferidos dependen de la magnitud de la tasa de migración de las poblaciones desconocidas.^[1] La técnica para derivar poblaciones fantasmas atrajo críticas porque las poblaciones fantasmas fueron el resultado de modelos estadísticos, junto con sus limitaciones.^[2]

Genética de poblaciones

En 2012, se utilizaron análisis de ADN y técnicas estadísticas para inferir que una población humana ahora extinta en el norte de Eurasia se había cruzado tanto con los antepasados de los europeos como con un grupo siberiano que luego migró a las Américas. El grupo se denominó población fantasma porque fueron identificados por los ecos que dejan en los genomas, no por huesos o ADN antiguo.^[3] En 2013, otro estudio encontró los restos de un miembro de este grupo fantasma, cumpliendo la predicción anterior de que habían existido.^[4]^[5]

Se analizaron la evolución de la proteína Mucin 7 en la saliva de los humanos modernos y se encontró evidencia de que una población fantasma no identificada de humanos africanos arcaicos puede haber contribuido con ADN, con un tiempo de coalescencia estimado para el ADN humano moderno de aproximadamente 4.5 millones de años AP, en el acervo genético de los africanos modernos (por ejemplo, Afroamericanos, Afro-Caribeños, Esan, Gambianos, Luhya, Mende y Yoruba).^[6]

Según un estudio publicado en 2020, hay indicios de que entre el 2% y el 19% (o alrededor de 6,6 y ≃7,0%) del ADN de cuatro poblaciones de África Occidental puede haber provenido de un homínido arcaico desconocido que se separó del antepasado de los humanos y neandertales hace entre 360 mil y 1,02 millones de años. Sin embargo, el estudio también sugiere que al menos parte de esta mezcla arcaica también está presente en euroasiáticos/no africanos, y que el evento o eventos de mezcla oscilan entre 0 y 124 ka BP, que incluye el período anterior a la salida de África y antes de la división africana/euroasiática (afectando así en parte a los ancestros comunes de africanos y euroasiáticos/no africanos).^[7]^[8]^[9] Otro estudio reciente, que descubrió cantidades sustanciales de variación genética humana no descrita anteriormente, también encontró variación genética ancestral en africanos que es anterior a los humanos modernos y se perdió en la mayoría de los no africanos.^[10]

En 2015, un estudio del linaje y la migración temprana del cerdo doméstico encontró que el mejor modelo que se ajustaba a los datos incluía el flujo de genes de una población fantasma durante el Pleistoceno que ahora está extinta.^[11]

Véase también

Linaje fantasma

Referencias

↑ ^a ^b Beerli, Peter (2004-04). «Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations». Molecular Ecology 13 (4): 827-836. ISSN 0962-1083. PMID 15012758. doi:10.1111/j.1365-294x.2004.02101.x.
↑ Slatkin, Montgomery (2005-01). «Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations». Molecular Ecology 14 (1): 67-73. ISSN 0962-1083. PMID 15643951. doi:10.1111/j.1365-294X.2004.02393.x.
↑ Patterson, N (2012). «Ancient admixture in human history». Genetics 192 (3): 1065-93. PMC 3522152. PMID 22960212. doi:10.1534/genetics.112.145037.
↑ Raghavan, M (2013). «Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans». Nature 505 (7481): 87-91. PMC 4105016. PMID 24256729. doi:10.1038/nature12736.
↑ Callaway, E (2015). «"Ghost population" hints at long-lost migration to the Americas». Nature. doi:10.1038/nature.2015.18029.
↑ Xu, D.; Pavlidis, P.; Taskent, O.R.; Alachiotis, N.; Flanagan, C.; DeGiorgio, M. (2017). «Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation». Molecular Biology and Evolution 34 (10): 2704-15. PMC 5850612. PMID 28957509. doi:10.1093/molbev/msx206.
↑ Arun Durvasula; Sriram Sankararaman (2020). «Recovering signals of ghost archaic introgression in African populations». Science Advances 6 (7): eaax5097. PMC 7015685. PMID 32095519. doi:10.1126/sciadv.aax5097. "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."
↑ Durvasula, Arun; Sankararaman, Sriram (2020-02). «Recovering signals of ghost archaic introgression in African populations». Science Advances (en inglés) 6 (7): eaax5097. ISSN 2375-2548. PMC 7015685. PMID 32095519. doi:10.1126/sciadv.aax5097.
↑ 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. PMC 7115999. PMID 32193295. doi:10.1126/science.aay5012. "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, Laurent A. F.; Schraiber, Joshua G.; Madsen, Ole; Megens, Hendrik-Jan; Cagan, Alex; Bosse, Mirte; Paudel, Yogesh; Crooijmans, Richard P. M. A. et al. (2015-10). «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. ISSN 1546-1718. PMID 26323058. doi:10.1038/ng.3394.

Datos: Q25304522

[:0-1] Beerli, Peter (2004-04). «Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations». Molecular Ecology 13 (4): 827-836. ISSN 0962-1083. PMID 15012758. doi:10.1111/j.1365-294x.2004.02101.x.

[2] Slatkin, Montgomery (2005-01). «Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations». Molecular Ecology 14 (1): 67-73. ISSN 0962-1083. PMID 15643951. doi:10.1111/j.1365-294X.2004.02393.x.

[3] Patterson, N (2012). «Ancient admixture in human history». Genetics 192 (3): 1065-93. PMC 3522152. PMID 22960212. doi:10.1534/genetics.112.145037.

[4] Raghavan, M (2013). «Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans». Nature 505 (7481): 87-91. PMC 4105016. PMID 24256729. doi:10.1038/nature12736.

[5] Callaway, E (2015). «"Ghost population" hints at long-lost migration to the Americas». Nature. doi:10.1038/nature.2015.18029.

[6] Xu, D.; Pavlidis, P.; Taskent, O.R.; Alachiotis, N.; Flanagan, C.; DeGiorgio, M. (2017). «Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation». Molecular Biology and Evolution 34 (10): 2704-15. PMC 5850612. PMID 28957509. doi:10.1093/molbev/msx206.

[7] Arun Durvasula; Sriram Sankararaman (2020). «Recovering signals of ghost archaic introgression in African populations». Science Advances 6 (7): eaax5097. PMC 7015685. PMID 32095519. doi:10.1126/sciadv.aax5097. "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] [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."

[9] Durvasula, Arun; Sankararaman, Sriram (2020-02). «Recovering signals of ghost archaic introgression in African populations». Science Advances (en inglés) 6 (7): eaax5097. ISSN 2375-2548. PMC 7015685. PMID 32095519. doi:10.1126/sciadv.aax5097.

[Bergstrom2020a-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. PMC 7115999. PMID 32193295. doi:10.1126/science.aay5012. "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, Laurent A. F.; Schraiber, Joshua G.; Madsen, Ole; Megens, Hendrik-Jan; Cagan, Alex; Bosse, Mirte; Paudel, Yogesh; Crooijmans, Richard P. M. A. et al. (2015-10). «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. ISSN 1546-1718. PMID 26323058. doi:10.1038/ng.3394.

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