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Exercise: Taxonomy


Written by: Rasmus Wernersson


Background

When comparing DNA and protein sequences from different species it is important to keep in mind that all living organisms at some point in time has shared a common ancestor. Some organisms are closely related and has recently derived from a common ancestor (e.g. Human and Chimpanzee, which diverged 5-10 million years ago) and some are more distantly related (e.g. Human and mouse, diverged 100-150 million years ago).

The more closely lated two organisms are, the less sequence divergence will be found (say, when comparing the Alpha Globin gene from each of the organisms), and the more likely it will be that similair looking genes from each organism still have the same function (MUCH more about this when we get to pairwise alignment and BLAST searches).

Apes taxonomy
(Detailed taxonomy of the Great Apes: Human, Chimp, Gorilla, Orangutan - from Wikipedia)


Phylogy vs. taxonomy

As we discussed in the lecture all life is organised in a hierachical taxomical system, which approximates the "true" underlying phylogeny to a large degree. It's therefore often important to know where a specific organism is placed in the taxonomical system - this type of information will also always be included along with DNA/Protein sequences from the big databases such as GenBank and UniProt.

Today we will explore various ways look up and compare taxonomy.

A word about Wikipedia

The free online encylopedia Wikipedia (and other similar resources) is a GREAT way to start out when you need to look up information about a new topic - in this case taxonomy. Almost all species entries in Wikipedia has a "Scientific classification" box which includes taxonomical information (for example see the entry on Orangutan or Fucus vesiculosus (Bladder wrack / Blæretang)).

HOWEVER: Keep in mind that Wikipedia is NOT a reliable source of information, even if most entries are of a very good quality. The facts in the Wikipedia entries has not been verfied by taxonomy experts and can potential be wrong (everybody can go in an edit the text). We need to look up the taxonomy in an official database (in this case we'll be using NCBI Taxonomy) before you can state it as a fact.

You CANNOT quote Wikipedia as the only source of your information - you'll need to find the original primary source of the information or look it up in an offical database.

Let me repeat that: "You CANNOT quote Wikipedia as the only source of your information".


The "Tree of Life" browser.

For the first part of the exercise we will be using the Tree of Life ("ToL") website to explore the taxonomy of various organisms. It's easy to step up and down in the evolutionary tree, and browse for interesting topics. Often a fair bit of in-dept information is provided at the various higher levels of taxonomy (for example "Mammals" or "Primates") - not only at the species level. ToL is also well illustrated with a lot of pictures and background material.

Tree of Life, overview picture



1) Open the Tree of Life website in a new browser windows/tab:  http://www.tolweb.org

2) Spend a few minutes investigating the general lay-out of the website and getting a feeling about what kinds of information are available. Notice that specific banches of the overall Tree of Life can be investigated by clicking directly on the tree on the main page.

3) Top-Down task: Investigate the taxonomical position of the domestic cat (Felis silvestris) by starting at the root of the tree and progressively going deeper into the sub-branches. (Danish note: "mammal" = pattedyr - "Placental mammals" er de pattedyr, der ikke er pung-dyr).

While you go from branch to branch scroll down the webpage to notice what kinds of information are provided (for example about evolution).

QUESTION 1:
  • Do you encounter any extint animal groups along your route to the felines?
  • How many species are listed with-in the genus Felis?.
4) "Bottom-up"-task:

Let's consider the following situation: you know that the scientific name of the domestic pig is "Sus scrofa" and you want to find out where it is placed in the taxonomical system.

  1. Search for "Sus scrofa" in the search-box at the top of the main webpage, and locate the page entitled "Sus scrofa".

  2. Now start walking "backwards" in the tree by clicking "Containing group".

  3. QUESTION 2a: What is the name of the first higher-level group? Does this makes sense considering the scientific naming scheme (the binominal names in Latin)?

  4. NOTICE: You can click the small tree icon in the upper left side to active the "quick navigation" menu. By "mousing-over" the icon a tool-tip about the function will be shown.

  5. QUESTION 2b: Continue navigating "backwards", until you encounter a the first taxonomical group that includes animals that are clearly not pigs. What is the name of this group?

  6. QUESTION 2c: Navigate all the way back to Eutheria (Placental mammals). Which (surprising?) group is the "sister group" to the one containing the pigs? (A sister group is the neighboring group in the tree - the most closely related group).
T. rex model
[Image source: Wikipedia]

5) Lastly we'll go dinosaur hunting in ToL. The task is to locate the famous Tyrannosaurus rex, and during the search we'll encounter an animal group that may be a bit of a surprise.

  1. Search for "Dinosauria".

  2. QUESTION 3a: There will be three sub-groups within Dinosauria. Are they all extinct?

  3. Continue "up" (high level -> low level) the tree until you reach Tyrannosauridae (there is a lot of information anout what defines a "Tyrant dinosaur" at this page). During the walk trough the tree notice what kinds of animals are included at the various levels of taxonomy - especially notice with groups are extinct and which are not.

  4. QUESTION 3b: Based on you observations: are all dinosaurs extinct?

  5. QUESTION 3c: Is the Black Bird a dinosaur - in the taxonomical sense?


NCBI Taxonomy Database

In the final part of the exercise we will be using the NCBI Taxonomy database. NCBI Tax is a more "dry" and techinical database, which contains accurate (standardized!) hierachical taxonomy of around 180.000 organisms. The NCBI Tax database also provides the numerical enumeration of species (and other taxonomical levels) that is used and referenced in most Sequence databases, such as GenBank (DNA) and UniProt (Protein). For example human (Homo sapiens) has the ID "9606" and Yeast (Saccharomyces cerevisiae) as the ID "4932".

NCBI Tax is not a database you would browse for fun (as you might with ToL). It's good for looking up definitions, and for comparing the taxonomical position of multiple organisms (since the information is so densely presented).

NCBI Taxonomy Logo

1) Open the NCBI Taxonomy webpage in a new browser window/tab: http://www.ncbi.nlm.nih.gov/Taxonomy/

2) Notice: a number of "popular" model organisms are linked directly from the main page.

3) Choose "Homo sapiens".

  1. Dont Panic: An enormous amout of information is shown - for example about genome sequences. In this case we only need to look at the Taxonomical information presented at the top of the page.

  2. Notice the Taxonomy ID - 9606 as mentioned above.

  3. "Lineage": Here the entire hierachical taxonomy is presented as a densly written list. Each taxonomical group on this list can be clicked and further investigated: first an overview page also containing 3 levels of sub-groups will be show - click the name again to get to the page dedicated to that entry.

    Notice that a large number of taxonomical groups are listed (including many "in-between" levels such as  "Craniata" (sub-phylum) and "Gnathostomata" (super-class). Most of these groups are simply left out in ToL for brievity.

    You can swith between showning ALL subgroups and a more condensed list by clicking "Lineage" - it will switch between "full" and "abbreviated".

    IMPORTANT: You can investigate the taxonomical rank of any group with out leaving the page by "mousing over" the text.

  4. QUESTION 4: What is the TaxID of "Metazoa"?

  5. Notice: It is in principle possible to browse the taxonomy by navigating deeper into the tree one step at the time (like with ToL) - however finding Human from the "Primates" level would require a lot of detailed knowledge about taxonomy and latin names for a lot of sub-groups.

    Click "Primates" from the Human entry and try to find out which group contains humans - you are on the right track once you get to the "Old world monkeys".
   
4) Comparing taxonomy using NCBI Tax.
Besides being useful for being the official database behind the TaxID's used in GenBank (and other databases), NCBI Tax actually makes it easy to compare taxonomy.

Let's take the situation where you have read an interesting paper comparing a DNA sequence between the following four organisms: Homo sapiens (Human), Mus musculus (Mouse), Danio rerio (Zebra fish) og Drosophila melanogaster (Fruit fly), but you have no idea about the relationship between the four organisms. We can look this up in NCBI Tax:
  1. Open two browser windows/tabs [http://www.ncbi.nlm.nih.gov/Taxonomy/] and search for Homo sapiens and Mus musculus.

  2. By comparing the "lineage" text it will be easy to find out at which taxonomical level human and mouse differ.

  3. QUESTION 5: Turn on "abbreviated" lineage information and find lowest ranking common group for human and mouse - what is the name and what is the rank?

  4. In order to get more information than just a latin name and a taxonomy rank, you can try to look up the group in a different database, such as ToL (NCBI will not reveal more than "placentals" if you investigate it further).

  5. NOTICE: Since a "user friendly" database such as Tree of Life doesn't contain the same amount of taxonomical groups, it may be necessary pick a group with higher rank if the first one is not found.
Zebrafish picture
Zebra fish [Image source: Wikipedia]
  1. Open a few more browser windows/tabs and find the information for Zebra fish and Fruit fly as well.

    Remember to turn on "abbreviated" lineage information for easy comparison.

  2. QUESTION 6: Which ranked group do connect Human and Zebra fish (ignore "no rank" groups)? Which rank? (You can look up this group in ToL for finding out more information).

  3. QUESTION 7: Which ranked group do connect Human and Fruit fly (ignore "no rank" groups)? Which rank? (As before furhter information can be gained from ToL).




Fruit fly picture
Fruit fly [Image source: Wikipedia]