Bottlenecks (or not) in human evolutionary history, as promised to Dorothy Heydt a year ago! (long)

Heya!

October last, there was a jolly interesting thread here on rassef-c
entitled "Predatory Characteristics of Humans". The discussion got onto
genetic bottlenecks - quoth I:

>I've seen several references about our having so many deleterious
>mutations being due to our having gone through a bottleneck about 100
>000 years ago, can anyone shed more light on this before I have to hit
>the journals?

To which Dorothy Heydt replied:

> There was a remark in the BBC series _Walking with Cavemen_ to
> there having been as few _H. sapiens_ around then, as there are
> orangutans today. So about 30,000.

> But I wouldn't call that a scholarly reference, much as I would
> like to (it was a neat series), so I fear you'll have to hit the
> journals ... let us know what you find out.

I said, Will do!

And then I went journal-surfing with the aid of my institution's
amazing-access-to-everything, which is quite capable of globally
hoovering all extant felidae simultaneously, and then I found some very
interesting papers indeed, and then I got lost in some otherwhere and
totally failed to report back.

And then I refused to let myself post here until I'd done that, but
every time I sat down with my .pdfs, something came up and I ended up
absconding awaywardly, and was thereby reduced to lurking on my
favourite group, which has been making my brain itch like crazy and
causing me to haunt Shwi too.

Anyway, only practically almost nearly a year later, I just wanted to
mention this paper:


Eswaran V, Harpending H, Rogers AR.
Genomics refutes an exclusively African origin of humans.
J Hum Evol. 2005 Jul;49(1):1-18.
PMID: 15878780 [PubMed - in process]


which I found absolutely fascinating as well as convincing - it seems to
show that there was no genetic bottleneck for Homo sapiens as such, but
rather that instead of modern humans expanding out of Africa and
replacing those less-advanced relations of theirs who'd spread outwards
before, it was the modern _characteristics_ which spread, at walking
speed, as people with them mated not just with each other, but also (if
less frequently) with their more primitive cousins.

The genes conferring the modern phenotypic traits conferred a greater
selective advantage than those that specified archaic traits, and thus
eventually replaced them within each population.

To begin with, in any location along the wavefront of the expansion of
modern traits out of Africa, there were only a few individuals with such
a phenotype, but then in each place, the proportion of the local
subpopulation which possessed them grew (slowly at first due to the
majority of children being born to modern-modern or archaic-archaic
couples rather than modern-archaic ones) until it reached 100%.

Thus, there were lots of *little* bottlenecks - one every time a clever
stranger from over the ridge married into the local tribe - which look
rather like one big bottleneck (a la cheetahs) if you don't consider the
characteristics which were _not_ replaced: the modern traits spread by
hybridization, but there were many genes in the population of humans who
first evolved a modern phenotype, which did _not_ spread, because they
did not confer a selective advantage in the other environments humanity
had spread to.

Some genes (the "modern" ones, and I'm not sure that I should just be
saying "allele" here, as I'm not at all convinced that it was all a case
of competing alleles - I think there were duplications given new
functions, etc.) spread, as they conferred an advantage in all the
places humanity had reached, but genes giving rise to adaptations to
local environments (and not conflicting with the adoption of modern,
more effective traits both anatomical and behavioural) were usually not
extirpated, but remained - and may even have been swept up in the
wavefront of modernity, and carried along with modern traits,
persisiting where they were useful.

The genetic variation caused by the assimilation of archaic traits not
associated with modernity, by itself suggests a multi-regional origin of
humanity, with humanity evolving in several geographically distinct
populations which were nonetheless linked by gene flow.

This paper, though, puts the hypothesis that some traits of humanity had
an African origin from which they spread, and that other traits evolved
elsewhere, and likewise spread, to a degree, but in different directions
and without always replacing their alternatives within the species.

The new globally-more-useful genes spread, and took with them whatever
they found along the way that was useful, for as long as it was useful.



(I think that's very far from the end of the story, though - I think new
alleles and genes have been whizzing round the world ever since, like
swords of Toledo steel, and that humanity is evolving at a furious rate,
driven by sexual selection and a pea***'s-tail like effect, with the
difference that what humans are using to out-do each other has more
practical uses too, such as building rocketships and spacesuits and
gengineering musk oxen over and over until you can call them Fuzzy
Britches and start a commercially successful radio show.)


Well, the above is my attempt to summarise eighteen pages of genomics
and statistics - you will have observed the clumsy language and clunky
sentence structure (which I'm telling myself are the result of my not
having slept for two days now rather than innate crapness), but I hope
you get the idea. (Please bear in mind that if any of the above looks
like nonsense, that's probably just my fault.)

The actual paper, naturally, puts it all much more clearly, subtly, and
to much greater depth, but I'm afraid you'd need access to _The Journal
of Human Evolution_, and if you don't have a site licence for it,
www.sciencedirect.com will let you look at the paper for $30, which is,
like fifteen quid on my side of the pond, and there's a new Ken MacLeod
out, and KJ Bishop's _The Etched City_ and that ace book _Jonathan
Strange & Mr. Norrell_ is probably right there with it and _Ash_ by
Gentle and _Gypsies_ by Wilson and Wolfe doing Severian in that very
same bookstore, along with a hundred other reasons why I'd be very happy
to email the paper (.pdf, 434KB) to any of you if you'd like to look at
it - just let me know!

(I don't think I'd be taking money away from the journal publishers or
anything, really...)

(Also, it occurs to me that there are groups on Usenet for posting
binaries - if someone could suggest a suitable one, I can post the paper
there and then come back here and tell everyone where it is. I guess it
depends how many people [if anyone] actually want a copy.)


I hope all that made sense - and that it manages to convey some fraction
of the excitement I felt upon finding a hypothesis that reconciles the
genetic evidence for Out Of Africa with that for the Multiregional
Model, explains a load a'stuff that'd been bugging me for years about
prehistory as normally presented, goes some way to explaining how
there's so much genetic diversity among Homo sap. and explains the
shadows in our past that from some angles look like bottlenecks or
xenocides.

(And I get to let myself delurk at last! Yay!)


Sincerely,

Johnny T.



PS--Abstract of paper:


Ten years ago, evidence from genetics gave strong support to the "recent
Africa origin" view of the evolution of modern humans, which posits that
Homo sapiens arose as a new species in Africa and subsequently spread,
leading to the extinction of other archaic human species.

Subsequent data from the nuclear genome not only fail to support this
model, they do not support any simple model of human demographic
history.

In this paper, we study a process in which the modern human phenotype
originates in Africa and then advances across the world by local demic
diffusion, hybridization, and natural selection.

While the multiregional model of human origins posits a number of
independent single locus selective sweeps, and the ??out of Africa??
model posits a sweep of a new species, we study the intermediate case of
a phenotypic sweep.

Numerical simulations of this process replicate many of the seemingly
contradictory features of the genetic data, and suggest that as much as
80% of nuclear loci have assimilated genetic material from non-African
archaic humans.

(Keywords: Modern human origins; Multiregional hypothesis; Out of Africa)
.