Using genealogical trees to examine admixture between modern humans and Neandertals

Thesis

This thesis uses genealogical trees to identify, date, and quantify patterns of admixture between Neandertals and individual modern human populations, using a combination of high quality data and parametric methodology. Previous methods on this subject have either approximated features of trees, or inferred them indirectly. Here, genealogical trees are used directly to understand the admixture process between humans and Neandertals by extending a recently developed method named CEPHi: Coalescent Estimation of Population History. CEPHi uses recombinationally cold regions of the human genome to build genealogical trees specifying the relationships between individuals in two input populations (one Neandertal, one human), including estimated population size histories, split times, and coalescence and mutation times.

Using CEPHi, a Neandertal-human population split time of ∼712,000 years in the past is estimated, as well as uncovering loci introduced by Neandertal-human admixture, revealing distinct bimodal distributions of estimated coalescence times between non-African and Neandertal haplotypes. A Neandertal population history is inferred, from the time of their split with humans up to ∼50,000 years ago (the fossil age), showing this archaic species to have suffered a bottleneck at this time, consistent with leaving Africa, followed by a further reduction to extinction.

Contrasting African-Neandertal and Eurasian-Neandertal analyses are used to define admixture using genealogical trees, and test our procedures in CEPHi via coalescent-based simulations. This region-level definition of admixture is used to specify sets of introgressed coldspots across 13 modern human populations. These sets are compared between pairs of populations, revealing information about the possible timing of interactions between Neandertals and modern humans, and sharing of admixture events between human groups, especially with respect to the split time between European and Asian populations. Online sets of introgressed regions for each of the four continents in our dataset are provided: African, American, Asian, and European.

Finally, in order to investigate the variation in time of contact between Neandertals and individual human populations, a novel method is described and implemented which dates admixture between individual human populations and Neandertals, using information from genealogical trees. Dates of admixture are estimated as ~50-60,000 years in the past in European populations, and ∼80-90,000 years in the past in Asian populations, suggestive of potentially somewhat distinct histories between European and Asian populations. This method can be applied to date any set of introgressed regions, including those shared between particular populations, enabling a clearer picture of the joint evolutionary history of modern humans, Neandertals, and other archaic species.

Authors: Frangou, A

• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford