The Iceman Preserved in GenGank

In the fall of 1991, hikers in the Alps found the frozen body of a man at the edge of a glacier which they took to be that of a recent victim of a climbing accident. In fact, the hikers had found the frozen, mummified body of a man who lived and died in the late Neolithic. Popularly known as the “iceman”, this well-preserved mummy and the artifacts found with him have provided an unprecedented and detailed view of human history, culture and biology of late stone-age Europe.

The well-preserved state of the mummy has allowed the collection of molecular sequence data that has shown the iceman’s relationship to modern Europeans and has provided insight into his diet and culture. Available sequences in GenBank include the iceman’s mitochondrial D-loop region as well as amplified sequences obtained in analyzing his artifacts, skin surface and intestinal content. Molecular data from the iceman are available in GenBank and integrated into the NCBI’s Entrez system.

The simplest way to find the sequences associated with the iceman is by linking to them from a PubMed search. Searching with ‘neolithic mummy’ finds a dozen articles at the time of this writing. Four of these articles link to sequence records in the nucleotide database. A more precise set of results can be obtained by using the filter that shows only articles with links to nucleotide sequences. The following query finds four articles reporting iceman sequences:

neolithic mummy AND “pubmed nucleotide”[Filter]

Figure 1. Display of four PubMed abstracts resulting from a query using the phrase 'neolithic mummy AND "pubmed nucelotide"[Filter]'. Each record contains links to corresponding data in other Entrez datasets, as shown from the Links menu.

In PubMed reference (4), Handt et al. report that the iceman’s mitochondrial D-loop (hypervariable control region) is consistent with the genetic variation of modern Europeans and is most similar to central and northern European populations. The nucleotide link from the PubMed summary leads to the iceman's D-loop sequence in GenBank record S69989. The Web BLAST service can be used to compare the iceman sequence to selected D-loop sequences from GenBank as shown in Figure 2 in which the iceman sequence is aligned to sequences from a modern European, AY041019, and from a Neanderthal human, AF254446.

The remaining three articles report analyses and identification of non-human DNA associated with the iceman’s body and clothing. A diverse taxonomic assemblage of sequences is linked to the PubMed reference (1) article, in which Rollo et al. reported the analysis of the iceman’s intestinal contents. These sequences provide a partial menu for the iceman’s last two meals and show the types of pollen present in his environment.

Following the nucleotide link from the PubMed summary of this article, displays the 15 sequence records reported. These are all conserved sequences of mitochondrial and chloroplast genes amplified by PCR. The biological origin of these sequences was inferred by sequence similarity. In most cases, the authors were able to assign organism sources only to higher taxonomic categories. The red deer (Cervus elaphus) and ibex (Capra ibex) sequences were confirmed by amplifying and sequencing them both from the iceman and from modern samples of the animals themselves. An interesting view of the taxonomic range of the organisms associated with the iceman with sequence data can be obtained by displaying all taxonomy links and creating a common tree within the Entrez taxonomy page.

Figure 2. BLAST alignment between the iceman's mitochondrial D-loop sequence, the Query sequence, and those of a modern human, AY041019, and a Neanderthal human, AF254446, respectively. The output shown was created by using web BLAST with an Entrez query to limit the BLAST database to the two target sequences. The results are presented in flat query-anchored format. The iceman sequence is identical to the modern and distinctly different from the Neanderthal sequence..

The authors show that some of the sequence signatures found, such as those for the deer and ibex meat and cereal grain (Triticeae), came from food items while others such as the pine (Pinus) and fern signatures were likely from unintentionally ingested pollen and spores.

Figure 3. A dendrogram showing the taxonomic classification of the DNA source organisms associated with the iceman.

The iceman has been touted by some as one of the most important discoveries of the century. Even though the iceman died over 5,000 years ago, his molecular legacy lives on at the NCBI.

—PC