Divergence and gene flow – what is a paleogenetic model

ResearchBlogging.orgWith the technical advances in gene sequencing, the possibilities of their use are growing rapidly. Totally new scientific disciplines evolve – eg the paleogenetics. Gene sequences are produced from bones thousands of years old, and these are compared with each other and with the gene records of living people. So kinship relations shall be found and the path of modern man in the conquest of the continents will be traced.

New disciplines employ best practices that are accepted by the community to secure their scientific approach. This applies not only to the claims of the exact and transparent working in the laboratory, but also for the methods to set up theories and to derive conclusions from theoretical assumptions. Parts of this scientific method are developing theories and build models. But what does that really mean, and what distinguishes a theory from a model?

David Reich and his team have carried out gene-sequencing of bones from a cave in Siberia (Denisova) (Nature 468, page 1053). The remains are approximately 30,000 to 50,000 years old. At that time in Europe and West Asia were living the “Neanderthals” while various hominins were represented in Asia. The gene sequencing showed that the Denisovians had a certain affinity with the Neanderthals, but also with the modern man. But how exactly looked this relationship? Were the Denisovians descendants of the Neanderthals, or were they a sister group?

To find answers to such questions, we first need a paleontological theory. Such a theory has an initial base, a foundation, and that is essentially the theory of evolution, especially the theory of mutations and re-combinations of genes. You have to be relatively safe what happens at the micro level, before you can set up theories on the macro level. Paleogenetics bases on the approach that similarities in gene sequences come from the same ancestral, while differences are explained by the fact that random mutations occur over time, which are combined through sexual reproduction steadily.

Part of the paleontological theory is that groups of individuals removed by migration from one another and do not mix anymore. Mutations are then spread only in one group and do not occur in the other. As these migrations take place over thousands of years but sometimes randomly change direction, such groups can also meet again and it is – scientifically speaking – time for “gene flow” between the groups.

From such a theory and the data of the gene-sequencing you can now build a “model of population history.” David Reich and his colleagues present a model that looks like this:

First, the ancestors of the Neanderthals separated from the ancestors of all living modern humans. Then the ancestors of modern Africans separated from those of all non-Africans, and about at the same time, the actual Neanderthals separated from the Denisovanern.

After the separation the “reunion” came – or at least something that was a “gene flow” between different groups. First, the Neanderthals met the ancestors of the non-Africans before they divided into various groups of people living today. One of these groups, the Melanesians met later the Denisovians, and again it came to the “gene flow”.

This model explains that Neanderthals have greater genetic similarity with non-Africans than Africans, and that the Denisovians are most likely to the Melanesians than all modern humans.

Such a model is of course an idealization, in which the researchers make decisions to fit the data in a clear structure. How long two populations have not had any contact so one can speak of a separation? How much they have to be met then again, so that a “gene flow” can bee identified? These questions can not be answered objectively, the answer is determined by how the empirical data can best be structured.

For the researchers in paleogeneticis who have sequenced the genes from the Siberian cave, the model is much like an idealized scenario, which ensures that the theory fits with the empirical data. One can imagine this model as a physical map of the world where small groups of figures to be pushed around. How they are able to move in principle, how they can split into sub groups and re-mix (and what happens to their genes) determines the theory. What do they really and where the actual figures really moved to (more precisely – how they are moved by the researchers, enacting his idea of the past here) is part of the model.

Are Reich and colleagues using the term “model” actually in the same sense as eg Physicists and other scientists do? This question I will first return, but in the next few weeks, I will publish more posts about theories and models in other disciplines in this blog, then hopefully a consistent picture of the scientific work in the tension between empiricism and theory, in which models may be as little as representing a mediating role, hoefully will appear.

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, & Pääbo S (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468 (7327), 1053-60 PMID: 21179161

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