Exploring taxonomy

 

Search with taxonomy

Background

Homo sp. Altai  (Denisova hominin) is an ancient hominin that was present in Eurasia at the time modern humans evolved 200,000 years ago. Denisovans share a common origin with Neanderthals, but are believed to have distinct morphological features and a separate evolutionary history. Mitochondrial DNA has been successfully sequenced from a finger bone and a tooth found in the Denisova Cave in Russia.

Scenario

Imagine you are digging in the Altai Mountains of southern Siberia, and in dark cave you find a fragment of skull bone. From the artefacts found near the bone, you believe you have found evidence of the Denisova hominin, but you can't be sure as past inhabitants of the region include Neanderthals and modern humans. You manage to isolate mitochondrial DNA and you want to compare it with other hominin species. You use EMBL-Bank to see what ancient DNA sequences from the genus Homo are available.

To search ENA for Homo sp. Altai sequence, type 'Homo Altai' into the text search box

Figure 55. To search ENA for Homo sp. Altai sequence, type 'Homo Altai' into the text search box.

Steps

1. Open the ENA Browser in a new window.

2.Type the search term Homo Altai into the text search box.

3. Click ‘Search’ to obtain search results.

Results - the Taxonomy Portal tab

The Taxonomy Portal provides a summary of the nucleotide data available for Homo sp. Altai.  You can now explore the data further by viewing the annotated nucleotide sequences or protein-coding sequences available, or you can use the Navigation tab to see what other ancient genomes are present in ENA.

Results page showing the Taxonomy Portal summary of the sequence data available for Homo sp. Altai

Figure 56. Results page showing the Taxonomy Portal summary of the sequence data available for Homo sp. Altai.

Notes

[A] Assembled Nucleotide Sequences (EMBL-Bank) shows all the annotated nucleotide and protein-coding sequences available for Homo sp. Altai.

[B] Portal tab provides a summary of all nucleotide data available for Homo sp. Altai, including unassembled data.

Steps

1. Expand the Taxa results to view the Portal tab displayed above.

2. Click on the Navigation tab.

Results - the Navigation tab

With the Navigation tab, you can easily browse the taxonomic tree. The results show that there is nucleotide data available for three species in the genus Homo: Homo sp. Altai, Homo sapiens and Homo sapiens neanderthalensis  (Figure 57).

The Navigation tab displaying the taxonomic tree for Homo sp. Altai

Figure 57. The Navigation tab displaying the taxonomic tree for Homo sp. Altai.

Notes

[A] Navigation tab displays a taxonomic tree for Homo sp. Altai, which can be navigated by expanding/collapsing the nodes in the tree.

[B]  The Homo [genus]  node has been expanded to show all the species in this genus with nucleotide data: Homo sp. Altai, Homo sapiens and Homo sapiens neanderthalensis.