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Old DNA Causes New Problems for Human Evolution

Recently, anthropologists set a world record when they isolated mitochondrial DNA from the 400,000-year-old femur of a Homo heidelbergensis specimen. The sequence of this DNA yielded a surprise for researchers when they discovered that it aligns more closely with that of the enigmatic Denisovans than with Neanderthal sequences. This latest work highlights the tentative nature of even the best ideas in human evolution.

As the old adage goes, “Never say never.” This maxim rings particularly true when it comes to the study of genetic material isolated from fossil remains. Just recently, a team of scientists from the Max Plank Institute in Leipzig, Germany (in collaboration with a team of anthropologists from Spain) recovered, sequenced, and analyzed mitochondrial DNA from a 400,000-year-old hominid femur.1 Prior to this work, the oldest DNA came from 100,000-year-old Neanderthal remains.

A few years ago, the idea of recovering DNA from fossil remains much older than 100,000 years would have been unheard of. Yet more sophisticated isolation methods, improved sequencing technology, and a better understanding of the chemistry of DNA degradation have all made this latest scientific feat possible. For a sampling of the key breakthroughs over the last decade or so in ancient DNA studies, as they relate to the hominid fossil record, check out the resources below:

The successful isolation and characterization of DNA from 400,000-year-old hominid remains is not the only unexpected outcome of this work. It turns out the mitochondrial DNA sequence is not what anthropologists anticipated it would be. Instead of aligning with Neanderthal mitochondrial DNA, the 400,000-year-old genetic material more closely matches the sequence of mitochondrial DNA assigned to the mysterious hominids known as the Denisovans.

The femur was part of an assemblage of fossils that represents 28 individuals assigned as either H. heidelbergensis or early Neanderthal. Researchers recovered the fossils in the early 1990s from a cave site in northern Spain, specifically from within a pit in the cave known as Sima de los Huesos (“the pit of bones”).

Some evolutionary biologists believe that H. heidelbergensis is the last common ancestor of the lineages that led to modern humans and Neanderthals. Others think that H. heidelbergensis is part of the Neanderthal lineage. In that case, the last common ancestor of humans and Neanderthals would most likely have been H. antecessor. Almost all evolutionary biologists believe the Neanderthal lineage later split to give rise to Neanderthals and Denisovans.

Based on these two evolutionary scenarios, anthropologists predicted that the mitochondrial DNA isolated from the femur would have Neanderthal characteristics. Instead, it appears as if the hominids represented by the femur were a sister group to the Denisovans and, thus, more closely related to these baffling hominids than to Neanderthals. In other words, the DNA sequences tell a different story than the fossils when it comes to the identity of the last common ancestor of modern humans and Neanderthals.2 In effect, this result stands as a failed prediction for one of the most prominent ideas in human evolution.

The authors of the research report suggest four possible ways to accommodate the unexpected result, but none of the scenarios work when all things are considered.3 The researchers write:4

Several evolutionary scenarios are compatible with the presence of a mtDNA sequence that falls on the Denisovan mtDNA lineage in a ~400,000-year-old hominin in western Europe. First, the Sima de los Huesos hominins may be closely related to the ancestors of Denisovans. However, this seems unlikely, because the presence of Denisovans in western Europe would indicate an extensive spatial overlap with Neanderthal ancestors, raising the question how the two groups could genetically diverge while overlapping in range. Furthermore, although almost no morphological information is available for Denisovans, a molar that carries Denisovan DNA is of exceptionally large size and does not exhibit the cusp reduction seen in the Sima de los Huesos hominins. Most importantly, the Sima de los Huesos specimen is so old that it probably predates the population split time between Denisovans and Neanderthals, which is estimated to one-half to two-thirds of the time to the split between Neanderthals and modern humans, which is estimated to be 170,000 to 700,000 years ago. Second, it is possible that the Sima de los Huesos hominins represent a group distinct from both Neanderthals and Denisovans that later perhaps contributed the mtDNA to Denisovans. However, this scenario would imply the independent emergence of several Neanderthal-like morphological features in a group unrelated to Neanderthals. Third, the Sima de los Huesos hominins may be related to the population ancestral to both Neanderthals and Denisovans. Considering the age of the Sima de los Huesos remains and their incipient Neanderthal-like morphology, this scenario seems plausible to us, but it requires an explanation for the presence of two deeply divergent mtDNA lineages in the same archaic group, one that later recurred in Denisovans and one that became fixed in Neanderthals, respectively. A fourth possible scenario is that gene flow from another hominin population brought the Denisova-like mtDNA into the Sima de los Huesos population or its ancestors. Such a hominin group might have also contributed mtDNA to the Densiovans in Asia. Based on the fossil record, more than one evolutionary lineage may have existed in Europe during the Middle Pleistocene. Several fossils have been found in Europe as well as in Africa and Asia that are close in time to Sima de los Huesos but do not exhibit clear Neanderthal traits. These fossils are often grouped into H. heidelbergensis, a taxon that is difficult to define, particularly with regard to whether the Sima de los Huesos hominins should be included. Furthermore, there may have been relict populations of still earlier hominins, notably those classified as Homo antecessor, which share some morphological traits with Asian Homo erectus and have been found just a few hundred metres away from Sima de los Huesos in Gran Dolina.

So, in effect the best explanation for these unexpected results is an appeal to interbreeding between the Sima de los Huesos hominids and an unknown hominid the researchers hope will be named at a later date.

This latest work highlights the uncertainty of even the best models in human evolution and the chaotic nature of the discipline. Perhaps this chaos is signaling the failure of the evolutionary paradigm to explain the origin of humanity. Yet, in the midst of these baffling results one thing seems certain—many anthropologists will never entertain the possibility that human evolution is false.

  1. Matthias Meyer et al., “A Mitochondrial Genome Sequence of a Hominin from Sima de lo Huesos,” Nature, published online December 4, 2013, doi:10.1038/nature12788.
  2. Ewen Callaway, “Hominin DNA Baffles Experts,” Nature, published online December 4, 2013,
  3. Normally, I would simply summarize each of the scenarios and point out the problems associated with each possible approach. However, I often find that skeptics accuse creationists of misrepresenting the views of evolutionary biologists. To avoid that accusation, in this case, I have decided to quote extensively from the original scientific paper.
  4. Meyer et al., “A Mitochondrial Genome Sequence.”