Counting the genetic ancestors from source populations in members of an admixed population

Agranat-Tamir, Lily; Mooney, Jazlyn A; Rosenberg, Noah A

doi:10.1093/genetics/iyae011

Cited by 3 publications

(1 citation statement)

References 23 publications

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“…Altogether, joint posterior estimation of numerous gene-flow rates parameters and the timing of their occurrence under highly complex demographic scenarios remains one of the most challenging tasks in population genetics. It will unquestionably benefit from future analytical theoretical developments (Mooney et al, 2023;Agranat-Tamir, Mooney and Rosenberg, 2024), and the improvement of machine-learning-based inference procedures (e.g. (Murtagh, 1991;Chen et al, 2020;Yelmen and Jay, 2023;Huang et al, 2024)).…”

Section: Conceptual Methodological and Empirical Limitations And Pers...mentioning

confidence: 99%

Ancient tree-topologies and gene-flow processes among human lineages in Africa

Breton,

Sjödin,

Zervakis

et al. 2024

Preprint

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The deep history of humans in Africa and the complex divergences and migrations among ancient human genetic lineages remain poorly understood and are the subject of ongoing debate. We produced 73 high-quality whole genome sequences from 14 Central and Southern African populations with diverse, well-documented, languages, subsistence strategies, and socio-cultural practices, and jointly analyze this novel data with 104 African and non-African previously-released whole genomes. We find vast genome-wide diversity and individual pairwise differentiation within and among African populations at continental, regional, and even local geographical scales, often uncorrelated with linguistic affiliations and cultural practices. We combine populations in 54 different ways and, for each population combination separately, we conduct extensive machine-learning Approximate Bayesian Computation inferences relying on genome-wide simulations of 48 competing evolutionary scenarios. We thus reconstruct jointly the tree-topologies and migration processes among ancient and recent lineages best explaining the diversity of extant genomic patterns. Our results show the necessity to explicitly consider the genomic diversity of African populations at a local scale, without merging population samples indiscriminately into largera prioricategories based on geography, subsistence-strategy, and/or linguistics criteria, in order to reconstruct the diverse evolutionary histories of our species. We find that, for all different combinations of Central and Southern African populations, a tree-like evolution with long periods of drift between short periods of unidirectional gene-flow among pairs of ancient or recent lineages best explain observed genomic patterns compared to recurring gene-flow processes among lineages. Moreover, we find that, for 25 combinations of populations, the lineage ancestral to extant Southern African Khoe-San populations diverged around 300,000 years ago from a lineage ancestral to Rainforest Hunter-Gatherers and neighboring agriculturalist populations. We also find that short periods of ancient or recent asymmetrical gene-flow among lineages often coincided with epochs of major cultural and ecological changes previously identified by paleo-climatologists and archaeologists in Sub-Saharan Africa.

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Section: Conceptual Methodological and Empirical Limitations And Pers...mentioning

confidence: 99%

Ancient tree-topologies and gene-flow processes among human lineages in Africa

Breton,

Sjödin,

Zervakis

et al. 2024

Preprint

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Bursts of coalescence within population pedigrees whenever big families occur

Diamantidis,

Fan,

Birkner

et al. 2024

Genetics

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We consider a simple diploid population-genetic model with potentially high variability of offspring numbers among individuals. Specifically, against a backdrop of Wright-Fisher reproduction and no selection there is an additional probability that a big family occurs, meaning that a pair of individuals has a number of offspring on the order of the population size. We study how the pedigree of the population generated under this model affects the ancestral genetic process of a sample of size two at a single autosomal locus without recombination. Our population model is of the type for which multiple-mergers coalescent processes have been described. We prove that the conditional distribution of the pairwise coalescence time given the random pedigree converges to a limit law as the population size tends to infinity. This limit law may or may not be the usual exponential distribution of the Kingman coalescent, depending on the frequency of big families. But because it includes the number and times of big families it differs from the usual multiple-merger coalescent models. The usual multiple-merger coalescent models are seen as describing the ancestral process marginal to, or averaging over, the pedigree. In the limiting ancestral process conditional on the pedigree, the intervals between big families can be modeled using the Kingman coalescent but each big family causes a discrete jump in the probability of coalescence. Analogous results should hold for larger samples and other population models. We illustrate these results with simulations and additional analysis, highlighting their implications for inference and understanding of multi-locus data.

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Nested admixture during and after the Trans-Atlantic Slave Trade on the island of São Tomé

Ciccarella,

Laurent,

Szpiech

et al. 2024

Preprint

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Human admixture history is rarely a simple process in which distinct populations, previously isolated for a long time, come into contact once to form an admixed population. In this study, we aim to reconstruct the complex admixture histories of the population of São Tomé, an island in the Gulf of Guinea that was the site of the first slave-based plantation economy, and experienced successive waves of forced and deliberate migration from Africa. We examined 2.5 million SNPs newly genotyped in 96 São Toméans and found that geography alone cannot explain the observed patterns of genetic differentiation within the island. We defined five genetic groups in São Tomé based on the hypothesis that individuals sharing the most haplotypes are more likely to share similar genetic histories. Using Identical-by-Descent and different local ancestry inference methods, we inferred shared ancestries between 70 African and European populations and each São Toméan genetic group. We identified admixture events between admixed groups that were previously isolated on the island, showing how recently admixed populations can be themselves the sources of other admixture events. This study demonstrates how complex admixture and isolation histories during and after the Transatlantic Slave-Trade shaped extant individual genetic patterns at a local scale in Africa.

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Counting the genetic ancestors from source populations in members of an admixed population

Cited by 3 publications

References 23 publications

Ancient tree-topologies and gene-flow processes among human lineages in Africa

Ancient tree-topologies and gene-flow processes among human lineages in Africa

Bursts of coalescence within population pedigrees whenever big families occur

Nested admixture during and after the Trans-Atlantic Slave Trade on the island of São Tomé

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