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 Omnis cellula e cellula.  (Every cell comes from a previous cell)

— Rudolf Virchow, 1855

 

As the HBO series Westworld put it so succinctly:  “Evolution forged the entirety of sentient life on this planet using only one tool… the mistake.”

A simple error in the code, one failure in a single transcription — otherwise known as a mutation — is the first turn of a Rubik’s Cube:  a statistical probability.  These simple errors in copying — given a template vast enough and a timetable long enough, passed on through countless generations of genetic code — can result in all the diversity of life we see around us today.  A mistake gives rise to change… change gives rise to diversity… diversity gives rise to competition… and competition gives rise to speciation.  Morgan Freeman made a similar Darwinian analogy with Christian Bale’s Batman giving rise to the Joker in The Dark Knight.  Evolution crafts and sculpts with the smallest of tools… but over a timetable that is unimaginably vast.  The fact that every brother and sister are not identical is proof that evolution is consistently at work.

“Over the course of four billion years, life has unfolded from minute specks indistinguishable from contemporary bacteria to great and integrated creatures, mushrooms and pterodactyls, whales and oak trees.”  — Franklin M. Harold, In Search of Cell History, p. 223

 

All mammals on the earth today can trace their lineage back to one little reptile living some 200 million years ago.  Before that all reptiles derived from one slightly divergent line of amphibian, and before that all amphibians derived from one slightly divergent line of fish.  And in this manner every class of life merges with another further back on the family tree.  Your DNA is ancient, built from four billion years of trial and error.

 

The chordate lineage in a nutshell: Flatworm > Fish > Amphibian > Reptile > Mammal.

 

How closely related are we to the other branches on life’s family tree?  Well, the evidence is in the DNA.  On the whole, you share roughly…

 
  • 99.95% of your DNA with your parents (you are effectively a clone)
  • 99.9% of your DNA with any other person on earth
  • 96-98% of your DNA with chimps
  • 90% with cats
  • 82-84% with dogs (sorry, dog lovers; cats win by a whisker)
  • 80% with cows
 

As a general rule, you may imagine any mammal to be 75% or more genetically identical to us, reptiles are under the 75% threshold, then amphibians in the 60s%, then fish, insects and invertebrates all lumping together by the low 50s.  Interesting aside:  we Homo sapiens are about 50% genetically indistinguishable from a banana.  Yes, you are half banana.  Or a banana is half you… I’m not sure which is more disturbing.  But this is why our bodies will more easily digest a hamburger than a salad… frankly, the hamburger is more closely related to us than the salad.  Thus it is easier for our bodies to turn the cow into human than it is for our bodies to turn a plant into human, as it is further removed from us genetically.

Parallels Between Language and DNA…

Evolution… descent with modification.  Every child looks like their parent, but not entirely; the detail is in that 50% of the .05% of difference.  Multiply this tiny difference by thousands of generations (… and billions of individuals…) and the variations begin to stack up.  Every person on earth — and that is to say, every face, every nose, every eye shape, every cheekbone and jawline; every feature found on anyone’s face today — represents a finished product of an unbroken chain of four billion years’ worth of evolution.  (That is, finished until the next generation continues to tweak it.)

But evolution isn’t just about slight modifications in the genome; it also benefits from isolation.  As we’ve learned in the past several decades, the tagline for evolution is less “survival of the fittest” as it is the real estate mantra… “location, location, location.”  Evolution and the emergence of new species (or “speciation”) is often determined by nothing more than gradual genetic drift.  Put simply, things left alone will go their own way.  How did evolution craft both chimps and humans — two entirely different species — from a common ancestor?  The short answer is geography.

Interesting thought experiment… if you were to take twin siblings — two genetically identical people — separate them geographically, marry them off and isolate them and all of their descendants in their respective small restricted genetic pools for 400,000 years or so, what would finally emerge after these million and-a-half generations would be essentially two different human species.  And make no mistake; they’d both be human, but they would be as different from one to the other as Neanderthals to us.  This is the inevitable consequence of genetic drift in isolation.

Really, the evolution of DNA may be compared to the way in which human language tends to evolve.  Words appear or disappear in isolated communities, meanings change, colloquial terms and different slang might arise.  The Romance languages that dominate Europe today — Spanish, French, Italian, Portuguese and Romanian — all descended from one mother tongue some 1500 years ago… common Latin.  All five of these languages branched out from one given nothing more than a slow-cooker of time and geography.

Language families are not unlike similar genetic haplogroups:  if any small population is cut off from another their DNA will gradually drift away from the other population, like any once-shared language will drift apart, until eventually — much as a different accents evolve into different dialects and finally into different languages — the two populations will head their way into entirely separate species if isolated long enough.  Human and chimp lines diverged some six million years ago, probably due to the geographic boundary presented by the Great Rift Valley.  The more recent split between the chimp line and the bonobo line two million years ago probably came about by a similar geographic boundary.  If one divergent group is not “brought back into the fold” (or cannot be, given geographic distances) that group simply continues to accrue genetic differences from any other, much like a fork in the road leads to paths that continue to diverge.

So to revisit the question above: if evolution is real then why would both chimps and humans thrive today; why was it not a wholesale replacement?  It’s for the same reason that the languages of Spanish and French thrive today; one did not replace the other, both derived from a common language and thrived in separate geographies.

Yet importantly, the same does not hold in regards to our species.  We replaced all of the other humans species.  What happened to the “missing links” in our evolution?  Are there really no closer surviving relatives to us today than chimps?  The answer is complicated; we’ll see shortly why this is so (and spoiler alert! … it involves a lot of sex).

Out of Africa…

So to be clear, we did not evolve from chimps, but instead we and today’s chimps evolved from a common ancestor.  Over the next three million years genus Australopithecus (which may be thought of as more ape than man) gradually gave way to genus Homo (more man than ape), but all of these early Hominins seem to have been confined to the African continent.  By about 1.8 million years ago Homo erectus became the first human species to migrate out of Africa, leaving behind in its wake a fossil trail discernible to us today; it is believed populations still existed in east Asia as recently as 50,000 years ago.  Erectus populations remaining in Africa largely gave rise to Homo heidelbergensis, which similarly began trickling out of Africa some 800,000 years ago.  Over a few hundred thousand years, those heidelbergensis populations that occupied Europe gradually became what we classify as Neanderthals, those in Asia became Denisovans, while those heidelbergensis remaining in Africa became… well, us.  Given enough time and geographic isolation, one human species just gradually became three.  We see what you did there, genetic drift in isolation.

So our species, Homo sapiens — anatomically modern humans/the last species standing today — emerged in Africa largely out of the heidelbergensis line between 300,000 and 200,000 years ago.  Our species began trickling out of Africa in miniscule migrations between 95,000 and 65,000 years ago.  The story of our species’ journey across the globe has taken place in a far shorter timetable (about a tenth of that heidelbergensis timeline), not enough to produce different species, but as anyone may attest, certainly different regional and geographic features.  Some 65,000 years ago all Homo sapiens were dark-skinned Africans; geography and climate have played a significant role in reshaping the human form as pockets of our species spread across the globe.  If the gene pool is the “hardware” of DNA, then think of the genetic responses to geographic and climate change as the “software patches”.  As populations of our species moved north their skin gradually lightened to filter in more necessary vitamin D, and conversely those who had been north for thousands of years and then headed south again (Polynesian populations, and Indigenous Americans — both North and South) began darkening once more.  Different features arose in different regions and formed the physical and cultural distinctions we still see today.

 Genetic variation is geographically structured, as expected from the partial isolation of human populations during much of their history.

— http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html

The worldwide human species on earth today is merely a snapshot; but it’s a perfect test-case of 65,000 years of genetic drift and varying degrees of geographic isolation.  Epicanthal eye folds, lactose-intolerance, skin tone and body stature; these are all just different evolutionary responses to different regional and cultural stimuli as humanity spread from one continent to six.

So do we know exactly which African population birthed the rest of today’s world?  Who were these bold pioneers who trickled out of Africa between 95,000 and 65,000 years ago?  We actually do know the answer, and DNA holds that clue.  As geneticist Spencer Wells and the Genographic Project demonstrated, all populations on this planet not living in Africa today can trace their genetic markers to the distant ancestors of the Khoisan people (the San Bushmen and the Khoikhoi people).  The buck stopped here.  This was the face of Homo sapiens some six hundred centuries ago, and these were the features that evolution would shape with great elasticity across the vast corridors of the earth.

 
Khoisan
They and you share a common ancestor; the face that spread over every corner of the earth
 

Perhaps the biggest surprise is not that we left Africa, but that it took us so long to do so.  Essentially, three quarters’ of our history as a species was spent in Africa.  One consequence of this is that we left much of our genetic diversity there.  In the words of paleoanthropologist Chris Stringer: “African populations have the greatest [genetic] diversity, and people outside of Africa are essentially a subset of that variation.” (Lone Survivors, p. 182)  All populations today living outside of Africa show a much lower genetic diversity, suggesting one or more “bottleneck effects,” as populations left Africa not in any big parade exodus, but in very small — even tiny — bands of families.

Simply, the entire population of the world today living outside of Africa came from small emigrations of isolated bloodlines.  Some 99% of Africa remained in Africa, the rest of the world today is made up of the 1% that left it.  It’s like pouring out a few jellybeans from a jellybean jar; the jellybeans that you’ve poured out of the jar are but a small sampling and would not include all the colors still residing in the jar.  Despite all the many superficial differences in the skin and faces between a person of European descent and a person of Asian descent today, the reality is that any child produced between them would STILL not possess the diversity found in an offspring from parents of neighboring communities in Africa.  In the case of those who left Africa, the sands of the DNA hourglass invariably narrow at that 65,000 year-old bottleneck, while African populations continued within the past 65,000 years a more free exchange of the older genes going back 200,000 years or more.

 
 

 The majority of the genetic polymorphisms found in our species are found uniquely in Africans.  Europeans, Asian and Native Americans carry only a small sample of the extraordinary diversity that can be found in any African village.

— Spencer Wells, The Journey of Man, p. 39

 Given its larger human populations and its greater continuity of occupation, Africa has probably always had more genetic and morphological variation than other parts of the inhabited world, giving greater opportunities for biological and behavioral innovations to both develop and be conserved.

— Chris Stringer, Lone Survivors, p. 219

To revisit the parallels between the evolution of language and the evolution of DNA, the ancient “Click” languages spoken by the Khoisan people show a very high complexity, a complexity that mirrors the higher genetic diversity found in their DNA.  “English, for example, has thirty-one distinguishable sounds used in everyday speech (two-thirds of the world’s languages have between twenty and forty), while the San !Xu language… has 141.  While it is uncertain exactly which forces govern the acquisition of linguistic diversity, this figure is certainly suggestive of an ancient pedigree — in exactly the same way that genetic diversity accumulates to a greater extent over longer time periods.” (The Journey of Man, p. 56)  Dr. Chris Stringer made a similar point in his Lone Survivors.  “Africa has the largest number and diversity of phonemes, and that number decreases as we move away from Africa.” (p. 218)  The language essentially mirrors the DNA.

How the horniest humans won the sex race…

So to revisit the above question,  what became of the world’s many “missing link” species?  After all, chimps are plentiful today, Australopithecines and other Hominins are decidedly… not.  So what’s the deal with that?

As populations of our species migrated out of Africa they encountered long-geographically separated cousins.  Some 65,000 years ago — the time at which our species was unquestionably roaming the earth — there were no fewer than four other human species existing outside of Africa:

  1. Neanderthals, in Europe
  2. Denisovans, in Siberia, central Asia and Polynesia
  3. remnants of Homo erectus still populated east Asia
  4. Homo floresiensis, in Indonesia

At least three of the four above would play a role in our narrative.  The old school of thought was that if there had been any interaction between our species and others outside of Africa it was limited interaction, perhaps even violent.  Now we know differently.  Where populations met they seem to have freely exchanged genes.  Wholesale genetic re-absortion took place virtually across the board.  Put plainly… we had sex with everyone.  I’ll leave floresiensis out of this equation because we don’t know enough about this rather diminutive and isolated species, but there is compelling fossil evidence to suggest that our species interbred with erectus in east Asia, while DNA evidence proves that we interbred extensively with Neanderthals and Denisovans.  At the same time, Homo sapiens reproduced prolifically and in numbers simply unmatched by the other populations.  Ultimately, there may be just two sex-related reasons why our species is the only one still standing today while the others are relegated to history.

  1.  We bred with them, and then…
  2.  … we outbred them in numbers they could not match.

Once upon a time (which is to say, before 2010) there was a general impression that perhaps our species had driven Neanderthals to extinction through competition or bloodshed.  The reality seems to be less R-rated violence and more R-rated gratuitous sex.  Over tens of thousands of years we absorbed them.  Simply, Homo sapiens won the sex race.

 Outnumbered 10 to one by modern humans, Neanderthals weren’t hunted to extinction by a supposedly superior species.  They were bred out, genetically swamped.

— PBS, Nova: Decoding Neanderthals, 2013

Currently, three human species have had their DNA sequenced and the genome decoded; the Homo sapien genome was finalized in 2003, the Neanderthal genome was published in 2010 and the Denisovan in 2012.  We have not yet retrieved DNA from Homo erectus or other older species.  What we have learned since 2010 though is that the DNA of today’s world population shows an eclectic mix of archaic admixtures, added to our genetic mix within the past 50,000 years.  Anyone of European or Asian descent today averages 2-3% Neanderthal DNA, while Tibetan/Melanesian populations today may show Neanderthal DNA… and an additional 2-5% Denisovan DNA.  According to 2021 research, the highest concentration of Denisovan DNA today is found in the Philippines.

It is important to note that in the case of Neanderthal DNA, the roughly 3% in my genome is not necessarily the same as your 3%, which is to say, we have different strings of code buried in our DNA.  If we were to compile together the DNA of everyone alive today, it is estimated that we could be able to reassemble roughly 30% of the entire Neanderthal genome.  Almost one-third of the Neanderthal genome is still active and being passed down through the living human population today.  The former blanket statement that Neanderthals went extinct must be revisited; it is about as accurate as saying the dinosaurs went extinct while ignoring the bird singing at your window.

Broad swaths of the world’s population today carry a legacy of Neanderthal and Denisovan DNA across the globe, to continents neither species ever saw or imagined, not unlike the lost luggage of a dead passenger traveling the globe from terminal to terminal long after his burial.

And even the African continent seems to have retained pockets of archaic humans within the past 50,000 years.  Wherever populations met, population-mixing seems to have occurred.  In the words of Chris Stringer, “sex happens.”  From his 2012 book Lone Survivors:  “[Current] African populations also contain about 2 per cent of ancient genetic material, and this was input some 35,000 years ago, not from Neanderthals or Denisovans but from an unknown archaic population within Africa itself, which might have been separate from the modern human lineage for some 700,000 years.” (p. 250, emphasis added)  Whether this genetic input was from heidelbergensis, erectus, or something more obscure or exotic within the pockets of isolation in Africa thousands of years ago, this finding just underscores the point that between Europe, Asia and Africa, gene pools separated by hundreds of thousands of years found a way to reconnect, even if only to re-establish a toehold.

The truth is, though we are the last human species on earth today, there was never any one lineage that resulted in the “us” of today.  The lines that lead to us were a porous, fluid and tangled tapestry; we are a mosaic of countless Homo and Australopith contributions.  We have a mutt heritage.

 Some of these evolutionary experiments died out, others came together and interbred.  The ebb and flow of these genes through these groups was probably so complex that we may have to give up hope of discovering a simple linear evolution.

— PBS, Nova: Dawn of Humanity, 2015

There were probably no fewer than 20 Homo species in Africa over the past two million years, and it does seem likely that every one of them may have contributed in some part to the bloodline that exists today.  There may be more than seven billion humans in the world now, but this is a recent trend; over the course of our ancestral history Australopithecines and early Hominins existed in perilously low densities.  We spent most of our history as an endangered species.  Early humans existed in small pockets, very much like chimp and gorilla communities today; isolated collectives with little interest in outsiders other than an occasional sexual encounter and exchange of genes.  The smaller these isolated groups, the more any outsider DNA would impact their gene pool.

The descent of Homo sapiens is not unlike someone’s genealogy of today, where despite your single surname there was no single line that made YOU; if you go back far enough, genealogical lines criss-cross, separate and actually merge again.  There are multiple rivers that flow into the gene-pool of you, and the further back you trace the streams, the more their courses branch, split, reconnect, narrow and broaden in unexpected ways.  Much like an all-female line resulting in the extinction of a surname, the “extinction of a species” is an arbitrary designation, because the DNA simply carries on, contributing to an individual or species no matter what name they might claim.  In this case, “extinction” simply juggles the proportions of the genetic mix.  Minute genetic contributions of archaic humans live on within our species today.  Homo sapiens may be “mostly derived” from Homo heidelbergenis in the same way that someone might be “mostly Irish” in heritage… the reality is more complicated.

My mom asked me once if evolution is over and I replied no; evolution never stops.  Descent with modification, after all, is just a consequence of sexual reproduction.  To bring back the Rubik’s Cube as an analogy, if each generation represents a single random twist of the Cube it is only a matter of time before any two cubes would cease to share the same colors.

A recent but notable mutation to have occurred is the existence of blue eyes, an adaptation well under a thousand generations old.  Blue eyes are related to a distinct mutation located in the OCA2 gene that first appeared between 6,000 to 10,000 years ago, and we can actually pinpoint this mutation to the geography of the Black Sea region.  “Blue-eyed Humans Have a Single, Common Ancestor” was a headline in January, 2008.  Blue eyes are an example of a genetic variation recent enough to be caught in the act, as it were, between being a regional feature and global one, widely in evidence in Europe and Scandinavia, but largely not yet introduced into indigenous populations of Africa, Asia or the Americas.  It might be odd to think of the spread of blue eyes in the same way one might think of the spread of a sexually transmitted disease, but it’s not an entirely inaccurate analogy.  Mutations are spread by sex.  The reality is that any two unrelated people of Western heritage today will likely share a common ancestor by 700 years ago, but a person of Western heritage and a person of East Asian heritage might not share a common ancestor before 40,000 years ago.  So mutations like the one in gene OCA2 have lacked the opportunity or timetable to enter that larger worldwide population before the advent of air travel.  Eye color, earlobes, toe lengths & wisdom teeth; these are all genetic features that are variable today.  These are transitional mutations.  The more variegated a species the more successful it is, and the more variegated the more variations it produces.  Evolution is an accelerated cycle.  Repetition leads to variation, and the larger the pool of repetition (i.e., the population) the more variations inevitably appear.  In short, not only are we still evolving but that evolution is accelerating the deeper the genetic pool becomes.

The Milestones that Made Us Human…

  • 8 million years ago — Genus gorilla (the ancestors of today’s gorillas) diverges from the line that would later produce chimps and humans.
  • 6 million years ago — The genetic lines that will comprise chimpanzees (genus Pan) and humans (genus Australopithecus) diverge from one another.
  • 3.2 million years ago — Today’s most famous Australopithecus specimen, Lucy, lives and dies without fanfare in East Africa.
  • By 3 million years ago — Studies examining the divergence between gorilla lice and human pubic lice suggest that the Australopithecines have lost most of their body hair by this point in time.
  • 2.8 million years ago — With a larger brain and a clear ability to fashion tools, genus Homo emerges out of the Australopithecus line.
  • Between 2.8 – 1.8 million years ago — A growing variety of Homo species, living in isolation much like communities of gorillas today, gradually absorb or simply replace Australopithecines throughout the African continent.
  • 2 million years ago — Homo erectus emerges, beginning a reign of two million years… representing the longest-lived and most successful human species (to date!).
  • 1.8 million years ago — Erectus begins migrating out of Africa, marking what is probably the first human exodus out of Africa.
  • Between 900,000 and 700,000 years ago — Homo heidelbergensis emerges, probably largely out of the African erectus/ergaster line.  Heidelbergensis populations spill out of Africa in another wave of human expansion.  Over the next several hundred thousand years these populations outside of Africa diverge into Neanderthals and Denisovans.
  • By 200,000 years ago — Anatomically modern humans — Homo sapiens (yes, our species) — emerge in East Africa, probably largely out of the heidelbergensis populations in Africa.  If this seems recent, it is… Homo sapiens arise out of the most recent 7.1% of the history of the Homo lineage.  So, 92.9% of human history predates our species, and for that matter, writing (recorded history) has only existed for 0.178% of human history.  Oh, somebody drag me away from this calculator….
  • Between 100,000 – 90,000 years ago — There is spotty evidence to suggest Homo sapiens are trickling out of Africa in early migrations.
  • Between 70,000 – 65,000 years ago — The ancestors of today’s world-wide genetically traceable population leaves Africa, but this total exodus would probably not account for more than 1% of the total Homo sapien population at the time, the bulk of our species (some 99%) remains in Africa, re-absorbing archaic human populations.
  • 40,000 years ago — There are no fewer than 5 human species living outside of Africa at this point in time:  Homo erectus populations still surviving in eastern Asia, Denisovans in the central Asia, Neanderthals in Europe and Homo sapiens.  Genetic evidence suggests interbreeding occurs sporadically (if not regularly) between Homo sapiens and the other three species, effectively and eventually absorbing them.  The fifth human species, Homo floresiensis in Indonesia, is a confusing outlier that we in the 21st century don’t yet understand (Is this a Homo erectus variant?  Does it represent a heretofore unknown Australopithicine emigration to Asia?  Did Homo sapiens ever encounter it?  We simply don’t know).