[SunkenCiv]

Alternatives to the Wright-Fisher model:
The robustness of mitochondrial Eve dating
Krzysztof A. Cyran and Marek Kimmel
online 19 June 2010

Abstract: Methods of calculating the distributions of the time to coalescence depend on the underlying model of population demography. In particular, the models assuming deterministic evolution of population size may not be applicable to populations evolving stochastically. Therefore the study of coalescence models involving stochastic demography is important for applications. One interesting approach which includes stochasticity is the O'Connell limit theory of genealogy in branching processes. Our paper explores how many generations are needed for the limiting distributions of O'Connell to become adequate approximations of exact distributions. We perform extensive simulations of slightly supercritical branching processes and compare the results to the O'Connell limits. Coalescent computations under the Wright-Fisher model are compared with limiting O'Connell results and with full genealogy-based predictions. These results are used to estimate the age of the so-called mitochondrial Eve, i.e., the root of the mitochondrial polymorphisms of the modern humans based on the DNA from humans and Neanderthal fossils.

Alternatives to the Wright-Fisher Model and Robustness of Mitochondrial Eve Dating
Marek Kimmel (joint work with Krzysztof Cyran)

Estimation of the time to the most recent common ancestor, or the so-called time to coalescence, is one of the most frequent procedures in population genetics. Several models for calculating the distribution of coalescence time exist, however their applicability is limited to a narrow spectrum of population trajectories. Also, they often rely on assumptions about generation to generation sampling scheme, known to be unrealistic for many populations, including the modern human population. We present a simulation-based approach capable of dealing with different population history scenarios, including populations evolving stochastically with environmental impacts variable in time. This approach allows comparing the branching process model of OConnell with a range of Wright-Fisher type models. We apply our approach to estimate the age of the most recent common female ancestor of humans based on the genetic material from mitochondrial DNA obtained from contemporary humans and extracted from Neanderthal fossils. The results indicate that when Neanderthals are used as an outgroup, the stochastic models based on branching processes provide similar estimates to those obtained with phylogenetic analysis, therefore supporting each other. On the other hand estimates assuming deterministic population growth are considerably higher, indicating that the stochastic demographic effects present in the human population when it was of a relatively small size are not negligible also for inferences dealing with long term history.

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Artist's cross section of a mitochondrion. (Credit: iStockphoto/David Marchal)

mitochondrial eve site:freerepublic.com

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[SunkenCiv]

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[null and void]

In before the first ‘they missed the date by 193,986 years’ comment...

[wildbill]

If we assume that all child-bearing ends at age 40, has anyone ever figured out how many ‘greats’ would go before grand mother after 200,000 years?

I’d like to address a prayer of thanks to my forebear.

[twhitak]

I thought she had a human father and a cylon mother.

[muir_redwoods]

I get this but it always begs the question; She did have a father and a mother of her own, right? wouldn’t her mother have beed due the honor?

[blam]

I wonder if it included the DNA of this recently found UNKNOWN human?

New Human Species Discovered: Mitochondrial Genome of Previously Unknown Hominins from Siberia Decoded

[Radix]

I wrote a paper on Mitochondrial Eve several years ago.

Nothing great, not Peer Review stuff, but still interesting.

Thanks for this and all of your terrific posts.

[mowowie]

Hey Civ, Thanks for ALL of these pings man.
There are a LOT of them! lol.
I don’t usually post but i read most of them.
Good Stuff.

[pabianice]

http://home.tiac.net/~cri_a/piltdown/piltdown.html

[antiRepublicrat]

[Doulos1]

Unverifiable, non-scientific, estimations, and ramblings.
Anything but the Bible, Alex, for $200.

[SunkenCiv]

• Human populations are tightly interwoven The most recent common ancestor of all humanity lived just a few thousand years ago, according to a computer model of our family tree. Researchers have calculated that the mystery person, from whom everyone alive today is directly descended, probably lived around 1,500 BC in eastern Asia...

[SunkenCiv]

This diagram works for most people, but not for folks with Down's Syndrome and a few other conditions. F is for father, M for mother; each of us has up to 64 great-great-great-great-grandcestors; no more than 46 of them has had even one chromosome pair reach you; even with the occasional crossing stream, there's no more than 46, and with crossing streams, could be less.

For those who don't know, this doesn't mean the other 18 (and all of their ancestors, plus half of the ancestors of the 46) are not your ancestors -- DUH! IOW, just because the chromosomes don't make it through, doesn't mean that Oetzi (for example) has no living descendants.

Grandma had no daughters (that lived); her brother was her only sibling; on her mother's side, I know only of a brother; etc etc...

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ggggGrand	gggGrand	ggGrand	gGrand	Grand	parents	YOU