Where did I come from?


Mitochondrial DNA and Human Evolution, again

Allan Wilson, working with research student Linda Vigilant and several other colleagues repeated the analysis of human genetic relationships. They changed several aspects of their study in response to criticisms of the previous study.

Use the maternal inheritance of mitochondrial DNA to estimate the genealogy of humans through the female line:

Human Groups Sampled
People from several geographic regions were represented in the study.

Africans, representing several sub-Saharan regions
Samples were taken from people in five different regions of sub-Saharan Africa, as shown in the map.

 

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©Charles Fred

African Americans
African American individuals were identified separately from sub-Sarahan Africans.

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Asians
People from China, Vietnam, Laos, the Philippines, Indonesia and Tonga.

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Caucasians
People from Europe

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©Delarge

Aboriginal Australians

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©mingzhuxia

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©k-girl

Aboriginal New Guineans

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©Kahunapule 
Michael Johnson

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©David Ringer

Tissues Used
A variety of tissues were used in this study. DNA was extracted from human placentas, as in the previous study. The methods for amplifying DNA from small samples had improved since that first study, so now DNA was also extracted from cultured cell lines, blood samples and hairs plucked from the scalp.

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Genetic Variation
The DNA sequence was determined for parts of the control region (also known as the D-loop) region of the mitochondrial DNA. These sequences were then aligned.

The DNA sequences were over 600 basepairs long with approximately 200 variable positions. This DNA alignment formed the basis of the analysis

Estimating the Tree
Genealogical or phylogenetic trees can be estimated from observed genetic variation because genetic change accumulates over time. There are different methods for estimating such trees. Some methods are based on average similarity or difference between pairs of sequences. The maximum parsimony was again used in this study. In this method many different possible trees are tested. For each tree, they ask "If this is the right tree, then how many evolutionary changes are required to explain the observed genetic variation?" The simplest explanation is considered the best. This means that the tree which requires the fewest number of evolutionary changes is the best estimate of evolutionary history. So, Wilson and colleagues searched for the tree which best explained the variation in DNA sequences among the individuals sampled.

The following diagram shows that in the left hand tree only one change is needed to explain the pattern of nucleotides observed at a given sequence position, but in the right hand tree two changes are needed. The parsimony method would choose the left had tree because it provides a simpler explanation of evolutionary history.

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As before, we need to be able to identify the point on the tree which represents the most recent common ancestor of humans, the root. The approach taken in the previous study was to put the root at the mid-point of the tree. This method was strongly criticised because it assumed an equal rate of evolution in all lineages. In this study, a Chimpanzee DNA sequence was added, as the outgroup. The common ancestor of humans and chimps will be somewhere on the branch separating the single chimp sequence and the human sequences. More importantly, the point where this branch joins the humans should represent the common ancestor of humans.

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References
This account is based on:
Vigilant, L., R. Pennington, H. Harpending, T. D. Kocher, and A. C. Wilson. 1989. Mitochondrial DNA sequences in single hairs from a southern African population. Proceedings of the National Academy of Sciences of the United States of America 86:9350-9354.
Vigilant, L., M. Stoneking, H. Harpending, K. Hawkes, and A. C. Wilson. 1991. African populations and the evolution of human mitochondrial DNA. Science 253:1503-1507.