What
has happened is that mankind entered the world of agricultural
abundance and is adapting to this new paradigm with a blast of
increased variation and choices. At present we are witnessing the
onslaught of global hybridization. This will shift variations across
huge populations and induce natural hybrid vigor world wide. It is
all stunningly efficient and we barely understand it is happening.
Add
to that our incipient capacity to outright manage desired outcomes
and we might expect to begin raising special purpose humans. As I
have already posted, I have conjectured that humanity did this
already some forty thousand years ago and then vacated the planet in
preparation for ending the Ice Age. They did it by the simple
expedient of ensuring the next generation was space adapted.
After
the Pleistocene Nonconformity had run its course from 13900 BP
through 10,000 BP, they then engineered another strain of humanity to
recolonize Terra and to terraform it.
What
has been done before will certainly be emulated as needed.
Human Evolution
Enters an Exciting New Phase
Brandon Keim
If you could escape
the human time scale for a moment, and regard evolution from the
perspective of deep time, in which the last 10,000 years are a short
chapter in a long saga, you’d say: Things are pretty wild right
now.
In the most massive
study of genetic variation yet, researchers estimated the age of more
than one million variants, or changes to our DNA code, found across
human populations. The vast majority proved to be quite young. The
chronologies tell a story of evolutionary dynamics in recent human
history, a period characterized by both narrow reproductive
bottlenecks and sudden, enormous population growth.
The evolutionary
dynamics of these features resulted in a flood of new genetic
variation, accumulating so fast that natural selection hasn’t
caught up yet. As a species, we are freshly bursting with the raw
material of evolution.
“Most of the
mutations that we found arose in the last 200 generations or so.
There hasn’t been much time for random change or deterministic
change through natural selection,” said geneticist Joshua Akey of
the University of Washington, co-author of the Nov.
28 Nature study. “We have a repository of all this new
variation for humanity to use as a substrate. In a way, we’re more
evolvable now than at any time in our history.”
Akey specializes in what’s known as rare variation, or changes
in DNA that are found in perhaps one in 100 people, or even fewer.
For practical reasons, rare variants have only been studied in
earnest for the last several years. Before then, it was simply too
expensive. Genomics focused mostly on what are known as common
variants.
However, as
dramatically illustrated by a landmark series of papers to appear
this year — by Alon Keinan and Andrew Clark, by Matt
Nelson and John Novembre, and another by Akey’s group, all
appearing inScience, along with new results from the
humanity-spanning 1,000 Genomes Project — common variants are
just a small part of the big picture. They’re vastly outnumbered by
rare variants, and tend to have weaker effects.
The medical
implications of this realization are profound. The previously
unappreciated significance of rare variation could explain much of
why scientists have struggled to identify more than a small
fraction of the genetic components of common, complex disease,
limiting the predictive value of genomics.
But these findings can
also been seen from another angle. They teach us about human
evolution, in particular the course it’s taken since modern Homo
sapiens migrated out of Africa, learned to farm, and became
the planet’s dominant life form.
“We’ve gone from
several hundred million people to seven billion in a blink of
evolutionary time,” said Akey. “That’s had a profound effect on
structuring the variation present in our species.”
Akey isn’t the first
scientist to use modern genetic data as a window into recent and
ongoing human evolution, nor the first to root rare variation in
humanity’s post-Ice Age population boom. The new study’s insights
reside in its depth and detail.
The researchers
sequenced in exhaustive detail protein-coding genes from 6,515
people, compiling a list of every DNA variation they found —
1,146,401 in all, of which 73 percent were rare. To these they
applied a type of statistical analysis, customized for human
populations but better known from studies of animal evolution,
that infers ancestral relationships from existing genetic patterns.
“There were other
hints of what’s going on, but nobody has studied such a massive
number of coding regions from such a high number of individuals,”
said geneticist Sarah Tishkoff of the University of Pennsylvania.
Akey’s group found
that rare variations tended to be relatively new, with some 73
percent of all genetic variation arising in just the last 5,000
years. Of variations that seem likely to cause harm, a full 91
percent emerged in this time.
Why is this? Much of
it is a function of population growth. Part of it is straightforward
population growth. Just 10,000 years ago, at the end of the last Ice
Age, there were roughly 5 million humans on Earth. Now there are 7
billion. With each instance of reproduction, a few random variations
emerge; multiply that across humanity’s expanding numbers, and
enormous amounts of variation are generated.
Also playing a role
are the dynamics of bottlenecks, or periods when populations are
reduced to a small number. The out-of-Africa migration represents one
such bottleneck, and others have occurred during times of geographic
and cultural isolation. Scientists have shown that when populations
are small, natural selection actually becomes weaker, and the effects
of randomness grow more powerful.
Put these dynamics
together, and the Homo sapiens narrative that emerges is
one in which, for non-African populations, the out-of-Africa
bottleneck created a period in which natural selection’s effects
diminished, followed by a global population boom and its attendant
wave of new variation.
The result, calculated
Akey, is that people of European descent have five times as many gene
variants as they would if population growth had been slow and steady.
People of African descent, whose ancestors didn’t go through that
original bottleneck, have somewhat less new variation, but it’s
still a large amount: three times more variation than would have
accumulated under slow-growth conditions.
Natural selection
never stopped acting, of course. New mutations with especially
beneficial effects, such as lactose tolerance, still spread rapidly,
while those with immediately harmful consequences likely vanished
within a few generations of appearing. But most variation has small,
subtle effects.
###
Visualization
of the distribution of potentially harmful genetic variation across
protein-coding portions of the human genome. The top section
represents variation that predates the human population explosion
10,000 years ago. The bottom represents variation that arose since
then. Image: Fu et al./Nature
It’s this type of
variation that’s proliferated so wildly. “Population growth is
happening so fast that selection is having a hard time keeping up
with the new, deleterious alleles,” said Akey.
One consequence of
this is the accumulation in humanity of gene variants with
potentially harmful effects. Akey’s group found that a full 86
percent of variants that look as though they might be deleterious are
less than 10,000 years old, and many have only existed for the last
millennium.
“Humans today carry
a much larger load of deleterious variants than our species carried
just prior to its massive expansion just a couple hundred generations
ago,” said population geneticist Alon Keinan of Cornell University,
whose own work helped link rare variation patterns to the
population boom.
The inverse is also
true. Present-day humanity also carries a much larger load of
potentially positive variation, not to mention variation with no
appreciable consequences at all. These variations, known to
scientists as “cryptic,” that might actually be evolution’s
hidden fuel: mutations that on their own have no significance can
combine to produce unexpected, powerful effects.
Indeed, the genetic
seeds of exceptional traits, such as endurance or strength or innate
intelligence, may now be circulating in humanity. “The genetic
potential of our population is vastly different than what it was
10,000 years ago,” Akey said.
How will humanity
evolve in the next few thousand years? It’s impossible to predict
but fun to speculate, said Akey. A potentially interesting wrinkle to
the human story is that, while bottlenecks reduce selection pressure,
evolutionary models show that large populations actually increase
selection’s effects.
Given the incredible
speed and scope of human population growth, this increased pressure
hasn’t yet caught up to the burst of new variation, but eventually
it might. It could even be anticipated, at least from theoretical
models, that natural selection on humans will actually become
stronger than it’s ever been.
“The size of a
population determines how much selection is going to be acting moving
forward,” said anthropologist Mark Shriver of Penn State
University. “You have an increase in natural selection now.”
An inevitably
complicating factor is that natural selection isn’t as natural as
it used to be. Theoretical models don’t account for culture and
technology, two forces with profound influences. Widespread use of
reproductive technologies like fetal genome sequencing might
ease selection pressures, or even make them more intense.
As for future studies
in genetic anthropology, Akey said scientists are approaching the
limits of what can be known from genes alone. “We need to take
advantage of what people have learned in anthropology and ecology and
linguistics, and synthesize all this into a coherent narrative of
human evolution,” he said.
Geneticist Robert
Moyzis of the University of California, Irvine, co-author of a 2007
study on accelerating human evolution, noted that the new study only
looked at protein-coding genes, which account for only a small
portion of the entire human genome. Much of humanity’s rare
variation remains to be analyzed.
Moyzis’ co-authors
on that study, geneticist Henry Harpending of the University of Utah
and anthropologist John Hawks of the University of Wisconsin, also
warned against jumping to early conclusions based on the new study’s
dating. Some of what appears to be new variation might actually be
old, said Hawks.
Even with these
caveats, however, the study’s essential message is unchanged.
“Sometimes people ask the question, ‘Is human evolution still
occurring?’” said Tishkoff. “Yes, human evolution can still
occur, and it is.”
Citations: “Analysis
of 6,515 exomes reveals the recent origin of most human
protein-coding variants.” By Wenqing Fu, Timothy D. O’Connor, Goo
Jun, Hyun Min Kang, Goncalo Abecasis, Suzanne M. Leal, Stacey
Gabriel, David Altshuler, Jay Shendure, Deborah A. Nickerson, Michael
J. Bamshad, NHLBI Exome Sequencing Project & Joshua M. Akey. Vol.
491, No. 7426, Nov. 29, 2012
