Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin Approaches
Ola Hössjer, Ann Gauger, Colin Reeves
In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).
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Genetic Modeling of Human History Part 2: A Unique Origin Algorithm
Ola Hössjer, Ann K. Gauger, Colin Reeves
This paper presents a mathematical unique origin model of humanity. It suggests algorithms for testing different historical scenarios of the human population under the assumption that we all descend from one single couple. For each such scenario, DNA variation is repeatedly simulated from a sample of individuals of today in order to estimate statistics of DNA variation. Comparison of these statistics to real data makes model validation possible. Each simulation repeat is divided into three steps, where first the genealogy of the sampled individuals is simulated backwards in time until the founder generation is reached, then founder DNA is generated and thereafter spread forwards in time to the present, along the lineages of the ancestral tree. The model is applicable to predefined demographic scenarios that may include population expansions and bottlenecks. Colonization/range expansion and geographic migration is achieved by dividing the metapopulation into geographically separated, but more or less connected, subpopulations. Age structure is modeled in terms of overlapping generations, with various mating rules for males and females and reproduction rules of mating couples. On the genetic level, our model incorporates mitochondrial as well as nuclear (autosomal, X and Y chromosomal) DNA, ordinary (reciprocal) recombination events and gene conversion. The source of genetic variation is selectively neutral germline mutations, and for autosomal and X chromosomal DNA, a second source of variation is created diversity. An extension of the model allows for balancing selection. It combines forward and backward simulation of the genealogy. Our paper is a first step towards a future goal to compare a best fitting unique origin model with a common descent model where humans and other species have a shared ancestry.
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