The Sciences

Ghosts in the Genome: Identification of an Unknown Fossil Hominid Through DNA Sequencing

The IntersectionBy Chris MooneyJun 17, 2010 3:36 PM


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This is a guest post from a member of Science in the News (SITN), an organization of PhD students at Harvard University whose mission is to bring the newest and most relevant science to a general audience. For over a decade, SITN has been presenting a fall lecture series at Harvard Medical School, with talks on a diversity of current and newsworthy topics, such as stem cell biology and climate change. SITN also publishes the Flash, an online newsletter written by graduate students at Harvard, which presents current scientific discoveries and emerging fields in an accessible and entertaining manner. SITN engages in additional outreach activities such as "Science by the Pint", and hopes students at other institutions will also make the commitment to strengthen science communication.

The following post is from Harvard graduate student Amanda Nottke.How Do We Identify Extinct Species? Paleontologists have always differentiated between extinct species by comparative anatomy of their fossil remains. Those scientists who study living organisms have an additional technique available – the comparison of DNA sequences between specimens. More recently, due to rapid advances in the efficiency and reduced cost of DNA sequencing, it has become possible to sequence DNA extracted from the remains of extinct species as well. This technology has been used on frozen mammoths recovered from ice, and from the bones of Neanderthals and ancient humans. Recently, the first complete Neanderthal genome was published, opening the way for multiple studies comparing us to our closest extinct relatives and shedding light on the fact that many modern humans carry 1-4% Neanderthal DNA; the result of ancient interbreeding events. These sequencing experiments have contributed much to our understanding of recent evolution, but until now they have been used as a support to the overwhelming fossil evidence, as opposed to a primary determinant of species identification. However, a discovery reported recently in the journal Nature is the first (to my knowledge) suggestion of a previously unknown species based only on their DNA. Even more fascinating, this species was a hominin, meaning part of the human family tree. The fossil itself was part of a finger bone excavated from a cave location in Siberia and estimated to be between 30,000-48,000 years old. Discovered in 2008, the finger was assumed to be from either a Neanderthal or an Anatomically Modern Homo Sapiens (AMHS, the scientific term for pre-civilization humans, our direct ancestors). It was a reasonable assumption, as these were the only two hominid species known to live in that geographical region at that time. Sequencing Ancient DNA: Why Mitochondrial? Of course, it is difficult to tell much about an individual based on a single fragment of a finger bone, so the scientists eventually decided to attempt sequencing its mitochondrial DNA to learn more about it. This type of DNA has two special properties that make it an appropriate target for sequencing ancient samples: its mode of heritability, and its amount. Mitochondrial DNA exists separately in the cell from nuclear DNA, which makes up the 23 pairs of chromosomes and nearly all the genes in the genome. Sperm carry nuclear DNA only, so mitochondrial DNA is inherited from your mother through the egg. Mitochondrial DNA is therefore commonly used in genealogical studies to trace matrilineal inheritance. In addition, it exists in hundreds or thousands of copies per cell, making it much easier for this type of sequence to be recovered after tens of thousands of years of degradation, as in the case of this particular fossil. The scientists used strictly sterile techniques to extract DNA from the Siberian fossil, to prevent contamination of the sample with their own mitochondrial DNA, and they sequenced it approximately 150 times over, to ensure the sequence was accurate. They also repeated the process independently using another portion of the fossil and got the same sequence, further supporting the accuracy of the sequencing. They then compared it to 54 samples of modern human DNA, 1 sequence from a 30,000 year old AMHS discovered in Russia, 6 Neanderthal sequences, 1 chimp sequence, and 1 bonobo (pygmy chimp) sequence. Not surprisingly, the Siberian specimen was extremely different from the two chimp sequences. An Unexpected Result But shockingly, the Siberian sequence was quite different from the other human and Neanderthal sequences as well. How different? On average, two modern human mitochondrial DNA sequences show 100 or fewer differences from each other. A Neanderthal sequence shows around 200 differences from a modern human, and a chimp shows almost 1,500 sequence differences from a modern human. The Siberian sequence showed almost 400 sequence differences from a modern human, and almost as many differences from a Neanderthal sequence. This mitochondrial DNA lineage was therefore most likely neither modern human nor Neanderthal. So what was it? Whatever it was, it shared a common ancestor with modern humans around 1,000,000 years ago, as calculated using the known rate of changes in the mitochondrial genome. Neanderthals are thought to have diverged only 500,000 years ago, meaning the Siberian lineage is not a Neanderthhal direct ancestor, and fits to no known fossil hominid. The scientists are careful not to conclude that this data is unambiguous evidence of an unknown hominid species. Because of the matrilineal inheritance of mitochondrial DNA, it is possible that this sequence is a remnant from a much earlier interbreeding event between earlier species, so that the Siberian specimen’s genome was nearly all modern human (or Neandertal) with only the mitochondrial genome maintaining its ancient sequence. Naturally, the scientists are now attempting to sequence the Siberian specimen’s nuclear genome, to determine whether those sequences match any known human or Neanderthal sequence. In parallel, paleontologists are searching for more fossil evidence that might support the identification of a new species. What will they find? We don’t know, but this sequencing result strongly suggests that an entirely unsuspected extinct human relative may have existed as recently as 30,000 years ago. The human family tree grows more and more complex with new discoveries, and this exciting coordination of paleontology and genetics is sure to uncover more unexpected surprises. 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