HUMAN MIGRATION TRACKED IN STANFORD COMPUTER SIMULATION

Stanford University Medical Center ^ | 21 January 2004 | Amy Adams

[PatrickHenry]

STANFORD, Calif. – Early humans migrating from Africa carried small genetic differences like so much flotsam in an ocean current. Today’s studies give only a snapshot of where that genetic baggage came to rest without revealing the tides that brought it there. Now researchers at the Stanford University School of Medicine have devised a model for pinpointing where mutations first appeared, providing a new way to trace the migratory path of our earliest ancestors.

The study was led by Luca Cavalli-Sforza, PhD, emeritus professor of genetics, who has spent most of his career tracking the evolution of modern humans. Much of his current work involves following mutations in the Y chromosome, which is passed exclusively from father to son, as humans migrated from Africa and spread to the rest of the world during the past 50,000 years.

These mutations, most of which cause no physical change, tend to appear at a constant rate, providing a genetic timer. For example, if a population has 10 mutations after 50,000 years of evolution from the common ancestor in Africa, then the fifth mutation probably arose 25,000 years ago. But where was the population located at that time? Until now genetics hasn’t had an answer.

“If we know the time when a mutation arose we know something. If we also knew the place we’d know almost everything,” Cavalli-Sforza said.

With the help of senior application software developer Christopher Edmonds and statistician Anita Lillie, both researchers at Stanford, Cavalli-Sforza built a computer model to simulate how mutations spread in a migrating population. The results of this work are published in this week’s online issue of Proceedings of the National Academies of Science.

The group reduced the world’s continents to a simple rectangular grid. They populated the first few squares with computerized human populations and gave those electronic villages realistic rates for population growth, migration and mutations. The inhabitants had more than one child, on average, and those offspring could migrate to any neighboring square as long as it wasn’t filled to capacity. This population growth filled the initial squares to capacity and pushed the computerized people to migrate at a constant rate across their rectangular territory until the next space was filled.

When a mutation appeared within a population, descendants reproduced and migrated at the same rate as other individuals. Most of the mutations, however, simply disappeared due to chance.

Those mutations that stayed in the population until the simulation ended showed one of two patterns. If the mutation appeared in a heavily populated area, it had a lower chance of surviving for many generations or reaching high numbers. In these cases, the mutation remained extremely rare in the local population.

If a mutation appeared in a person at the edge of the migration front where the population was scarce, the mutation was more likely to spread through the population. The mutation-carrying person multiplied and the offspring migrated, taking the mutation to neighboring squares. If these neighboring squares were previously unoccupied, the mutated person had a high probability of reproducing and passing along the mutation. The mutation itself remained most common in the migratory wave front, a situation Cavalli-Sforza refers to as “surfing” the migratory wave.

Over the course of 64,000 simulations, the group came up with a model for finding a mutation’s origin. First they identified the mutation’s farthest edge – corresponding with a boundary such as the ocean or mountain range in human populations. Then they calculated the average area of where the mutation is distributed – called the mutation’s centroid. According to the models, the centroid is about half the distance between where the mutation arose and where it ended up.

In at least some simulations, the mutation no longer existed in the population where it first arose. Without the group’s way of estimating distance, there might be no trace of the mutation’s place of origin. Now they can generate a dated “we were here” sign to place on the route of human migration.

[PatrickHenry]

Everybody be nice.

[PatrickHenry]

PING. [This ping list is for the evolution side of evolution threads, and sometimes for other science topics. FReepmail me to be added or dropped.]

[Republic If You Can Keep It]

The assumption here seems to be that the origin of humankind was in Africa.

Is that the majority opinion now? Are there any knowledgeable dissenters?

Just curious.

[Doctor Stochastic]

Nice article. I'll check the original later today. I find it interesting (meaning I hadn't already thought of it) that mutations that occur on the boundaries spread more widely than those at the center. It would be fun to do a similar model with linguistic chances (the Great Vowel Shift, Grimm's Law, The Great Germanic Consonant Shift, etc.)

I wonder what they used for "neutral" migration (unpressured by population, etc.) I would guess that a diffusion (random walk) would be a reasonable migration model in the absence of barriers.

[Right Wing Professor]

The assumption here seems to be that the origin of humankind was in Africa.

If I may...

There is no doubt we came out of Africa at some stage. There is some dissent about whether modern humans are entirely descended from humans that left Africa within the last 100,000 years, or whether there is some genetic contribution from the Neanderthal or Homo erectus populations that inhabited Eurasia previous to that, and may have been there for over a million years.

[Moonman62]

I thought this was going to be another thread about amnesty.

[buffyt]

There was a special on TV about this. They actually traveled from Africa, up through Europe, over to Alaska, where you used to be able to walk across when there was a land bridge, then down through Canada, USA, and SA. It was very interesting.

[expatpat]

I think it's accepted. Both the y chromosome track through males and a corresponding track through females lead to Africa. The Y chromosome method (where you track the mutations back into the past) leads to a (Bantu?) tribe who use clicks for communication.

Interestingly, these folks don't look like sub-Sahara faces (thick lips, dark skin) but have a variety of facial types, many looking like eskimos and central asians.

Apparently our aancestors migrated out of Africa, through the middle east, and stayed a while in central asia before spreading out to Europe, Siberia, and the Americas.

[nightdriver]

It could be argued that his model for migratory pressure is flawed, if human nature is to be considered. Humans are much more ambulatory than the study would intimate, certainly over the long periods of time under study.

His study would probably be more accurate for colonies of bacteria.

[DoctorMichael]

Interesting. Bttt

[Alamo-Girl]

Thanks for the ping!

[Doctor Stochastic]

Ok, now that I read the original, it's even better than the publicity blurb.

[observer5]

This entire this is horse-s*it.

100% Pure Speculation

[Pharmboy]

Population Bottlenecks and Pleistocene Human Evolution
John Hawks,* Keith Hunley,† Sang-Hee Lee,‡ and Milford Wolpoff†
*Department of Anthropology, University of Utah; †Department of Anthropology, University of Michigan; and ‡Department
of Biosystems Science, Graduate University for Advanced Studies, Kanagawa, Japan
We review the anatomical and archaeological evidence for an early population bottleneck in humans and bracket
the time when it could have occurred. We outline the subsequent demographic changes that the archaeological
evidence of range expansions and contractions address, and we examine how inbreeding effective population size
provides an alternative view of past population size change. This addresses the question of other, more recent,
population size bottlenecks, and we review nonrecombining and recombining genetic systems that may reflect them.
We examine how these genetic data constrain the possibility of significant population size bottlenecks (i.e., of
sufficiently small size and/or long duration to minimize genetic variation in autosomal and haploid systems) at
several different critical times in human history. Different constraints appear in nonrecombining and recombining
systems, and among the autosomal loci most are incompatible with any Pleistocene population size expansions.
Microsatellite data seem to show Pleistocene population size expansions, but in aggregate they are difficult to
interpret because different microsatellite studies do not show the same expansion. The archaeological data are only
compatible with a few of these analyses, most prominently with data from Alu elements, and we use these facts to
question whether the view of the past from analysis of inbreeding effective population size is valid. Finally, we
examine the issue of whether inbreeding effective population size provides any reasonable measure of the actual
past size of the human species. We contend that if the evidence of a population size bottleneck early in the evolution
of our lineage is accepted, most genetic data either lack the resolution to address subsequent changes in the human
population or do not meet the assumptions required to do so validly. It is our conclusion that, at the moment,
genetic data cannot disprove a simple model of exponential population growth following a bottleneck 2 MYA at
the origin of our lineage and extending through the Pleistocene. Archaeological and paleontological data indicate
that this model is too oversimplified to be an accurate reflection of detailed population history, and therefore we
find that genetic data lack the resolution to validly reflect many details of Pleistocene human population change.
However, there is one detail that these data are sufficient to address. Both genetic and anthropological data are
incompatible with the hypothesis of a recent population size bottleneck. Such an event would be expected to leave
a significant mark across numerous genetic loci and observable anatomical traits, but while some subsets of data
are compatible with a recent population size bottleneck, there is no consistently expressed effect that can be found
across the range where it should appear, and this absence disproves the hypothesis.

[CobaltBlue]

Based on analysis of mitochondrial DNA, it is presently believed that the ancestors of all humans alive today are descended from people who were alive in Africa some 75,000 years ago.

That does not necessarily mean that human beings originated in Africa, only that our own ancestors did. Given that humans have existed for much longer than 75,000 years, a lot could have happened during the time before 75000 BC that we don't know about.

[CobaltBlue]

It's not just one study, there are a lot of studies, all over the world.

I have ordered a kit to have my own mitochondrial DNA tested It's all the rage with genealogists. My own DNA will tell me whether it's true that my great-great-grandmother was half Native American. If the roots go directly to Europe, then it's probably not true. Actually I might have my mother take the test, our mitochondrial DNA will be identical (more or less) and my siblings would probably get more out of it symbolically coming from her than from me.

I am going to get a nuclear DNA (Y-chromosome) kit as well as a mitochondrial DNA test for my dad.

[Doctor Stochastic]

Not a bad article either. It doesn't have much relation to the original posting though. The bibiliography of the article in your post is pretty good.

[whattajoke]

This entire this is horse-s*it.
100% Pure Speculation

Thank you. Your reasoned, well written, intelligent response to the original article will cause the scientists behind the study to re-think their position.

[txhurl]

Sound like fun. Wouldn't it be great if the results read: you are a descendent of the Rockefellers.

[Pharmboy]

He had asked for anyone who disagrees with the conventional thinking on out of Africa--Wolpoff is the man; the other point is that the bottlenecks throw out the genetic figuring--which is relevant here.

Best,

PB