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Evolution basics: Becoming human, Part 3: Paleogenomics and the tangled web of human speciation

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June 5, 2014 Tags: Genetics, History of Life, Human Origins
Evolution basics: Becoming human, Part 3: Paleogenomics and the tangled web of human speciation
Photo credit: North Carolina School of Science and Mathematics (Creative Commons BY-NC-SA 2.0)

Today's entry was written by Dennis Venema. You can read more about what we believe here.

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we discuss how genome sequencing of extinct hominin species both clarifies and complicates our understanding of human speciation.

In previous posts in this series, we’ve sketched out the general outlines of hominin evolution – the hominins being those (extinct) species more closely related to us than to our closest living relative, the chimpanzee. And as we have seen, the hominin family tree was at one time diverse, with numerous species overlapping in both time and geographical distribution.

Hominin phylogeny
A hominin phylogeny based on current paleontological – and in some cases, genomic – evidence. Genome sequences are available for humans, Denisovans, and Neanderthals. See this prior post for more details.

Of particular interest is the fact that this pattern of contemporaneous hominin species extends to humans: we coexisted with other hominin species for tens of thousands of years. The geographical and temporal overlap between humans and Neanderthals, for example, has long been known. What remained unknown – and highly contentious – was the question of interbreeding between humans and extinct hominin groups. Did humans and Neanderthals have children together? Did some of those children remain with human populations and become ancestors of some modern humans? Such questions are nearly impossible to address using only fossil remains (especially since Neanderthals and humans are so similar to begin with). Genetics, however, could provide a definitive answer – and developments in genomics technology would be the key to solving the puzzle.

The rise of (paleo)genomics

It’s sometimes difficult as a scientist to communicate with my friends just how rapidly the science of sequencing entire genomes has advanced over the last decade or so. When I was a graduate student in the late 1990s, even my model organism of choice (the lowly fruit fly, Drosophila melanogaster) had not yet had its genome completely sequenced. At that time, the human genome project was underway, but years from completion. Genome sequencing was the stuff of “big science”: large, well-funded groups spending millions upon millions of dollars to slowly piece together the data bit by painstaking bit.

Of course, when the scientific community makes such a significant investment it pays dividends far beyond the data itself: we also become much more technologically capable in the relevant area. In a decade, genome sequencing went from expensive, cutting-edge big science to an inexpensive, largely automated technique. Not only did genomics become much, much cheaper, it also became increasingly sensitive: we gained the ability to assemble genome data from ever smaller amounts of DNA.

Eventually, these advances would allow us to isolate and sequence DNA from extinct species. Amazingly as it sounds, in the proper conditions DNA can persist inside bones and teeth for tens (or even hundreds) of thousands of years. Given our interest in human evolution, DNA sequencing of Neanderthals was one of the first uses for this new technology – and for the first time we could test the hypothesis of interbreeding with genetic evidence.

All in the family – or not?

The first Neanderthal DNA to be sequenced was their mitochondrial DNA, which, as you may recall, is maternally inherited(i.e. passed down from mother to daughter, but not through males). These early studies found that Neanderthal mitochondrial DNA was not passed on into modern human populations. This in and of itself did not rule out the possibility of interbreeding, since mitochondrial DNA lineages can easily be lost in a population, and interbreeding involving male Neanderthals would not introduce Neanderthal mitochondrial DNA into human populations in the first place.

Later work sequencing Neanderthal chromosomal DNA would provide the definitive test, and the results were stunning: some modern human populations do have Neanderthal ancestry. As humans migrated out of Africa around 50,000 years ago, they encountered Neanderthals in what is now the Middle East. This encounter included (relatively rare) instances of interbreeding between the two groups. Moreover, we know that at least some of the children of human / Neanderthal matings remained within the human population, and went on to have children of their own. Today, traces of Neanderthal DNA can be found in all modern humans who are not of sub-Saharan African ancestry. Since sub-Saharan Africans descend from a population that did not encounter Neanderthals, they lack the characteristic Neanderthal DNA variation seen in other human populations.

More data, more evidence of interbreeding

Though the Neanderthal genome was first published in 2010, we have made significant advances in understanding patterns of hominin interbreeding even since then. One such advance was the discovery of a previously unknown hominin group, dubbed the Denisovans, which we know of from only a few finger bones and teeth. These meager remains were nonetheless able to provide a complete Denisovan genome sequence, and reveal them as a relative of Neanderthals. The Denisovan genome also revealed that they too contributed DNA to some modern human populations, specifically those of Melanesian descent.

Even more recent work has sequenced a high-quality Neanderthal genome. Though we have long had a relative abundance of Neanderthal remains, their DNA quality is poor. The discovery of Neanderthal remains in the same location that preserved the exceptional Denisovan DNA at last provided a very high quality Neanderthal genome, the analysis of which was published just this year. This new data allowed for several more robust analyses comparing human, Denisovan, and Neanderthal genomes. These analyses produced several noteworthy results: modern mainland Asian populations also have a small amount of Denisovan DNA; humans contributed some DNA variation to Neanderthals; Neanderthals and Denisovans interbred, with DNA variation flowing both ways; and (perhaps most interestingly) Denisovans have DNA variation that suggests they interbred with yet another archaic hominin group, possibly Homo erectus.

From these results, we can revisit the branching tree of hominin species and recognize that the pattern is not as simple as we have represented it. The general outline and relationships haven’t changed, but instead of clean divisions into separate lineages we now need to envision the branching pattern as more web like, with genetic exchange between what we previously represented as entirely distinct species. As we continue to find new hominin remains and (hopefully) sequence DNA from them, it is likely that the pattern will become even more webbed, adding detail and complexity. Just like a historian discovering ancient texts and exchange between ancient languages, so too we can now see the patchwork makeup of our own genome, and that of our close relatives.

Phylogeny showing hominin relationships
Hominin relationships and approximate divergence times for lineages leading to Neanderthals, Denisovans, and modern humans. Paleogenomics has revealed this branching pattern to have a more web-like structure, with limited interbreeding between these groups.

Of course, biologically speaking, these findings further complicate the expectation of finding a “first human” above and beyond the usual issues associated with gradual change of a species over time. Modern humans are one species, but nonetheless have subtle genomic variation derived from regional encounters and genetic exchange with a number of related hominins that diverged from our lineage and left Africa prior to our geographic expansion. As scientifically fascinating as these results are, these findings are naturally of theological interest for Christians as well – a conversation that is just beginning in evangelical circles, and will likely take some time to develop.

For further reading

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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GJDS - #85620

June 5th 2014

The extraordinary confidence displayed in these posts on evolution and related subjects leaves me astonished. I would suggest that those interested in understanding the details of science, without adopting an ideological stance in discussions that seek to mix faith and evolution, may be well served by critically reading on the subject. And again I emphasise that I avoid referring to papers/articles that seek to argue for or against the many claims made for neo-Darwinian thinking, but instead read papers that clearly support the Darwinian view. This is to make sure that I have not brought in any attitude other than scientific curiosity. So in this vane, I quote from Rizzi et al. Genetics Selection Evolution 2012, 44:21.

One common feature of ancient DNA samples is the presence of miscoding lesions that cause the incorporation of incorrect nucleotides during DNA amplification. In 2001, Hofreiter et al. showed for the first time that most of these damage-derived errors are caused by hydrolytic deamination of cytosine into uracil leading to apparent C->T or G->A substitutions in DNA templates sequenced after PCR amplification. To reduce the number of such misincorporations, assays involving pre-treatment of ancient DNA samples with uracil N-glycosylase have been conducted to remove uracil residues from the DNA sequence and leave abasic sites that prevent replication by the Taq polymerase during PCR. However, the use of uracil N-glycosylase has not been widely adopted in studies with ancient DNA, because the number of template molecules in such samples is often so small that the enzyme may destroy all the amplifiable templates.”

The paper is a review of the methodologies that have been developed over decades, which to varying degrees, try to reconstruct or amplify ancient samples that clearly have undergone transformations. While these techniques are interesting and workers are constantly seeking to improve their methods, it is axiomatic that the sample integrity for any analysis is the prime concern for a scientist. This means that the more ancient the sample, the greater the uncertainty and error that is inherent in any analysis. When we consider the complexity of cells, DNA, and related matters in bio-specimens, a very healthy skepticism is highly desirable.

Steve Sterley - #85627

June 6th 2014

> The extraordinary confidence displayed in these posts on evolution and related subjects leaves me astonished. I would suggest that those interested in understanding the details of science, without adopting an ideological stance in discussions that seek to mix faith and evolution, may be well served by critically reading on the subject.

And I suppose you think creationist literature is objective and fair? Have you ever spent 5 minutes critically evaluating their claims and looking up their sources to see whether they agree?

The fact that there is an overwhelming consensus amongst scientists who produce papers like the one you quoted from should tell you something. They read the same scientific papers that you claim to read “objectively” and yet they have the same confidence that DV has in the fact that we are closely related to Neanderthals and Denisovans.

Finally, I would imagine that the problem you raise would only be an issue if they had a single set of chromosomes from a single nucleus to analyse since if there was degradation, the same sequence would be degraded in different ways within different cells.

In the paper Dennis mentioned, the sample was obtained from a toe and would have covered the chromosomes from millions of cells. The sample was also “high-quality” (unsurprising - it was found in Siberia) presumably meaning that the results they obtained from multiple copies of each sequence were largely in agreement.

GJDS - #85634

June 6th 2014

“And I suppose you think creationist literature is objective and fair? Have you ever spent 5 minutes critically evaluating their claims and looking up their sources to see whether they agree?”

You should note that I have stated that I stay away from literature that deals with your US culture wars, and I again say that I am interested in how science is done. I am a practicing scientist and I have stated on many occsions that I bring the same critical outlook to papers dealing with Darwinain outlooks, that I bring to my own papers, and the ones that I review in my field. Since biology is not my field of research, I have made it a point to only look through papers that do not show a bias for or againat creationism - this is why I am often surprised by the responses I have recieved by some on this site. The paper I have referred to reviews this area, and gives imo a fairly balanced view on the methodology and thinking in the area covered by this blog. The review also mentions previous conclusions that were subsequently shown to be wrong regarding ancient samples of DNA.

Any scientist, whatever his worldview, would stop and examine the vast conclusions often made by those with an ideological agenda - it is not how many samples they can obtain for their testing, but the nature of the sample after it has been ‘standing’ for many thousand of years, and the way that sample has to be conditioned to obtain some information. I have dealt with thousand of samples, some of which need to be analysed down to ppm and ppb by the most modern techniques available, and I am fully aware of the difficulties we face when we ‘push’ any method to its extremes; as I have said, the most critical aspect of stringet analysis is the sample, where and how it is obtained and how representative it is of the subject investigated.

I suggest you read the paper I have referred to (and any other paper you may consulst) and then give informed opinions on the ‘quality’ of sample, methodology, and data; after that we may have an informed discussion on the conclusions one may and may not draw from such, and the confidence we may have regarding such.

Steve Sterley - #85647

June 7th 2014

> Any scientist, whatever his worldview, would stop and examine the vast conclusions often made by those with an ideological agenda - it is not how many samples they can obtain for their testing, but the nature of the sample after it has been ‘standing’ for many thousand of years

What ideology? The paper Dennis mentioned was published in a scientific journal (Nature) and it was peer reviewed (not by arm-chair critics but by actual geneticists who are familiar with the potential pitfalls)

Regardless, this doesn’t address my point which is that if they have many-fold coverage of a given sequence, then they can elminate errors due to hydrolytic deamination.

Perhaps it would also help if you read the paper Dennis mentioned? Not only did they have 52 fold coverage, but they applied the exact method suggested in the paper you linked to to avoid this error.

From the paper Dennis mentioned:

We generated four DNA libraries using a recently published protocol that is particularly efficient in retrieving DNA from ancient samples. These libraries, together with one library prepared using a previous protocol, were treated with uracil-DNA glycosylase to remove uracil residues, a common miscoding lesion in ancient DNA that results from the deamination of cytosine (Supplementary Information section 5a). In total, these five DNA libraries provided 52-fold sequence coverage of the genome. We estimated present-day human DNA contamination in the libraries with four complementary approaches (Supplementary Information section 5) using mtDNA and nuclear DNA and conclude that present-day human contamination among the DNA fragments sequenced is around 1%. After genotype calling, which is designed to be insensitive to low levels of error, we expect that the inferred genome sequence is largely free from contamination.

What is it exactly that you are getting at anyway? Are you trying to argue that humans and Neanderthals don’t share a common ancestor?

GJDS - #85652

June 7th 2014

This is the type of discussion that may prove useful - I have commented previously that I have not inferred that papers such as these, are deliberately erronious - in fact I have inferred the opposite. It is within this context that I have examined a range of papers and have been convinced that much of what is portrayed as scientific fact and certain, is often an inferrence which is grounded in a larger Darwinian context. As an example, I have shown from other papers that the information/data may has been reported as incomplete and the authors than look to other sources to bolter their position/conclusions. My overall view has been that studies in the bio-sciences are far more complicated and demanding that say chemistry and physics, and the past has shown that people have rushed to decalre their finding as facts and certainty of science, when they were not.

To put is as simply as I can, anoter paper that presents the most uptodate study on common ancenstry for a large number of species, provides a pictorial representation of this common ancestor, and a range of characteristics, including the time scale when it should have existed and so on. With so much certainty in these observations, it is necessary, for this to be scientifically verified, for the researchers to present some bones, or fossils, or scientific evidence to prove as a scientific fact that it existed, let alone give rise to so many other species. This is what is termed a scientific verifiable and testable fact.

If this cannot be done, it does not invalidate the work of these people - but it MOST CERTAINLY refutes claims that their conclusion has been verified, tested, and can claim to be a scientific fact. It may be inferre, and some people may believe the opinions put forward - they are not however, ‘facts of science’.

I remained astonished that these relatively straighforward aspects of science appear to be unaccptable to some people who comment on this site.

James Stump - #85807

June 18th 2014

NOTE:  Some replies to this comment were removed.

GJDS - #85653

June 7th 2014

“..not by arm-chair critics but….”

I agree that I am an arm chair critic; in fact my inital comment on this site is to show that I (and many others) carry out our research without referring or requiring Darwin’s semantic theories - and we are happy with this, and I have not as yet been berated by bio-scientists for this. This comment is to show in a light hearted manner that Darwin’s thinking is not the be all and end all of the Sciences, and on occasions I have pointed out that many practicing bio-sciences have expressed reservations on the seemingly huge claims made on Darwinian outlooks.

Again, I have no religious objections to geological time scales and what have you, nor that many species have existed over such time periods. In an area that I am active, we have a number of theories that involve geological time scales, and we work hard to arrive at mechanisms that may account for our observations - I can assure you, there is a great deal we cannot explain or understand. I for one am happy to acknowldege this - it does not destroy faith where it is found - but I suggest some people are more interested in conflict and try to claim science as a weapon. In the Orthodox Christian I would be hard pressed to find anyone who is bothered by Darwinian outlooks.

Thus do not get aggrivated or upset - my comments about certainty and uncertainty in the sciences are not that controversial (again I acknowledge that I have made many typo errors in these hastily writen posts).

PNG - #85629

June 6th 2014

GJDS, you have expressed your misgivings about all attempts to think about how modern scientific results might fit together with a Christian perspective, even such relatively straightforward matters as noting that the Big Bang cosmology seems to fit nicely with (and make a rather wry understatement of) “Let there be light.”

Surely, we should expect that eventually a theological perspective, if it is true, should eventually fit together in some respects with a scientific one. Do you think that all such efforts are unwise?

Bobsie - #85661

June 8th 2014

Just a quick point of clarification; the BB did not release any “light” until the Recombination at ca 377K years post BB when the universe went from opaque to transparent with the formation of hydrogen and helium atoms. So at best, “Let there be light” had a significantly delayed fulfillment. Just saying.

Jimpithecus - #85635

June 6th 2014

Some general thoughts on this information from a post on my site:  “So, if the split between modern humans and Neandertals was around 600 Ky B.P., who would have been the progenitors of these groups?  Modern humans don’t appear on the landscape until between 160 and 190Ky B.P.  Neandertals don’t appear until maybe 300 Ky B.P.  Here is one possible scenario. Sometime prior to 600k B.P., there was a migration out of Africa by one or more groups of archaic Homo sapiens/late Homo erectus.  This explains the similarities between the Petralona and African Kabwe crania, as well as that of the Gran Dolina remains and the African Bodo cranium.  In Africa, the archaics went about their business being archaic until around 200 ky B.P., when the modern genome began to arise (in response to what?).  In Europe, over time, in the face of not one but two ice ages (The Riss and Würm), one group evolved into the Neandertals, who’s remains are found in Europe, the Levant, northern Iraq and very western Russia. Populations in the two areas would have, depending on the level of gene flow in the circum-Mediterranean area, become genetically isolated. Now here is the really odd thing.  When these groups reunited, so to speak, they discovered that, not only was there an attraction, they were still genetically compatible after some 500 thousand years apart—to a point. Even though they actually produced viable offspring (and the presence of Neandertal genes in modern humans demonstrates that they were), because the Neandertal and modern human genomes were “optimized” if you will, eventually over time, hybrid depression would likely have ensued, reducing the fitness of the hybrid offspring.  This may account for the ultimate demise of the Neandertals, who had a genome that, with the warming at the end of the early Würm stadial, was likely undergoing negative selection pressure.  If, in fact, there was a swamping of the Neandertal genome by arriving moderns through the gates of Europe, this would have sped up the process.”

Jimpithecus - #85636

June 6th 2014

The only thing I don’t like about the above scenario is that it assumes somewhat restricted gene flow between the European and North African groups.  That may be reflected by their general geographic separation, though in the sense that, once the people were in Europe, very few people got south and even fewer people got north.  Maybe.

Jimpithecus - #85637

June 6th 2014

One more comment about the above scenario: It is bare bones at best but explains much of the fossil data.  It leaves aside the hotly contested notion of whether or not Neandertals were a separate species from the early moderns and, with them, reflected a syngameon, or whether, as Milford Wolpoff contends, they reflect a widely polytypic species that interbred at the peripheries.

Jimpithecus - #85638

June 6th 2014

The point is, there is quite a bit of other evidence from the fossil record and the archaeological record to support what Dennis is writing.

sy - #85651

June 7th 2014


I think your scheme makes a lot of sense. I would add a comment related to your question regarding the rise of the modern human genome at 200 kya “In response to what?” Rick Potts has found a fascinating series of major fluctuations in humidity in the Rift Valley region going back about a million years, and including (I believe) the critical period from 400 to 200kya. One could imagine a great deal of selection pressure from this ongoing environmental stress in Africa. 

Im not sure if this has been published yet (the general idea of rapid and fluctuating climate change as a stimulus to human evolution has been); I heard Potts speak about a month ago and the data was quite exciting. 

Jimpithecus - #85662

June 8th 2014

Thank you for that.  I need to look that one up.  And thank you for getting the discussion back on track.

Jimpithecus - #85863

June 24th 2014

Morphological support for this model!!  http://www.sciencedaily.com/releases/2014/06/140619142204.htm

James Stump - #85680

June 9th 2014

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