Decoding Our Family

This year has been a significant one in the world of primatology.  Field and lab studies have revealed insight into the origins of bipedalism, cultural complexity, tool construction and shelter construction.  However, the biggest news has come from genetics: the last two great ape genomes (gorilla and bonobo) were sequenced in their entirety (the first human genome was sequenced in 2000, the first chimp genome was sequenced in 2005 and the first orangutan genome was sequenced in 2011).  So now that the human genome and all of the great apes genomes have been sequenced, what have we learned?  Did genome sequencing reveal any surprises about our evolutionary history with our closest relatives?  Well, I’m going to try and break down some of the deepest evolutionary insights gained from decoding our family.

Evolutionary history

Decoding the human and great ape genomes has finally given us definitive answers regarding great ape relatedness and critical past speciation events.  During the 19th and early 20th century many evolutionary theorists could tell that great apes were our closest relatives but there was still debate regarding who we were most closely related to and what continent our species evolved on.  Although Charles Darwin believed our closest relative was the chimpanzee and our home continent was Africa, others thought our closest relative was the orangutan and our home continent was Asia, and embarrassingly, some argued that our home continent was Europe based on the fraudulent Piltdown Man skull.

Throughout the 20th century, phenotypic and geographical evidence from known fossil humans indicated that our closest common ancestor was with chimpanzees and bonobos and our home continent was Africa, however, since sequencing all great ape genomes, we now have the undeniable proof.  For example, the genome sequencing attempts has revealed that we differ from chimpanzees and bonobos equally by 1.3%, while we differ from the Asian orangutans by 3%.  Interestingly, we also gained insight into relationships between the great apes themselves, for example we now know that chimpanzees and bonobos only differ by 0.4% of their genomes.

Now I must take a second to note that simply knowing the percentage two organisms differ isn’t all that is important about the genome; it is also important to know:

  • What genes are being activated at what time during development
  • Percentage of genetic difference or similarity that is from ‘junk DNA’ (DNA that does not code for anything)
  • Specific information on what is different about the genes that are not shared and when they were selected for

There are several great examples of why it is important to know this information, instead of simply relying on the overall percentage of genetic similarity:

  • All breeds of dog differ very little (<0.2%) in overall genetic sequence variation yet show considerable phenotypic variation
  • Chimpanzees and humans have the same amount of overall genetic sequence variation as the two mouse species, Mus musculus and Mus spretus, yet those two mouse species look identical, whereas chimpanzees and humans differ substantially in phenotypic variation
  • And my all-time favourite – humans are about 50-60% genetically similar to a banana

However, knowing the difference our genomes vary is still an important piece of knowledge, because it does show us the overall pattern of relatedness and allows us to estimate timing of speciation events.  Before all the great apes had their genomes sequenced best estimates on speciation dates were drawn from fossil evidence (which are almost non-existent for our closest relatives).  From this evidence general consensus was that our common ancestor with chimpanzees and bonobos split 4 million years ago (mya), our common ancestor with gorillas split 8 mya and our common ancestor with orangutans 12 mya.  Now that we can compare genomes, these dates have all been adjusted and pushed back.  The genetic evidence indicates that we share a common ancestor with chimpanzees 6 mya, gorillas 10 mya, and orangutans 15mya.

So the picture of our evolutionary past has become a lot clearer because of the genetic evidence.  This has implications for palaeoanthropology because it means that we now have a strict window for investigating candidate common ancestor species with our closest living relatives.  It also means that species we considered candidates in the past (e.g., Lucy (Australopithecus afarensis)) have now been reintegrated into a new narrative of human evolution that extends its roots back an extra 2 million years.

Here are a list of species we have found around the temporal range we would expect the speciation event to have occurred:

Sahelanthropus tchadensis (7mya) (Central Africa)
Orrorin tugenensis (6mya) (Eastern Africa)
Ardipithecus kadabba (5.8-5.2mya) (Eastern Africa)
Ardipithecus ramidus (4.5-4.3mya) (Eastern Africa)

Orrorin is looking pretty good at the moment.

Pace and quirks from the past

But the genome sequencing taught us more than just relatedness and speciation events.  The evidence can also give us insight into the pace of evolution and some interesting evolutionary quirks hidden in our genes.

For example, the orangutan genome has shown us that the pace of evolution for them has been glacial, whereas the pace of evolution for chimpanzees, bonobos and humans has been comparatively fast.  There are several hypotheses that have been suggested to explain these findings.  It could be that orangutan evolution has been slow because both species of orangutan have been isolated on islands throughout their history (Sumatra and Borneo) and consequently, neither species has needed to adapt to a significantly different environment.

Analysis of the genomes has also shown us that some speciation events have been messier than others.  For example the bonobo-chimp split seems to have been very sudden, abrupt and clean.  This means that when the common ancestor of the chimpanzee and bonobo split there was no further interbreeding.  This lends support the hypothesis that Congo River acted as a natural barrier to migration for both chimpanzees and bonobos.  However, we do know that not all speciation events were so clean.  In fact, the human-chimp-bonobo split appears to have been far less abrupt and may have been a slow speciation that spanned a million years or more.  This means that a permanent ecological barrier was likely not responsible for the speciation event.

Some odd quirks of the past have also been revealed in the early years of great ape genome analysis.  Perhaps one of the more interesting finds is that gorillas and humans share a considerable number of functional genes that chimpanzees do not have.  One of these genes is LOXHD1  which is responsible for human hearing.  Researchers in the past hypothesized that this gene must have been selected for during the development of complex language.  However, if gorillas also possess this gene and it is expressed at similar frequencies, this cannot be the case, unless gorillas are keeping their ability to use complex language a secret.

Family decoded

Although our family has now been decoded there is still much more research to be completed and much more to know about our evolutionary history and our shared ancestry with the great apes.  Genomes are very large, and it is not clear what the function of all expressed genes is.  Furthermore, much of the questions that were answered by sequencing the great ape genomes have raised more complex questions that require more data and more hypothesis testing to resolve.  But one thing is clear, by decoding our family we have gained a better sense of who we are and where we came from.

 

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About Cadell Last
Hello. I'm probably drinking coffee and reading.

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