Using the Taxonomy database ANSWERS: Difference between revisions

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=Answers to the [[Taxonomy databases|Taxonomy exercise]]=
=Answers to the [[Using_the_Taxonomy_database|Using the Taxonomy database exercise]]=


Answers by: Rasmus Wernersson  
Answers by: Rasmus Wernersson and Henrik Nielsen. Last update: Aug 2026
   
   
==Question 1:==
== Question 1:==
=== a)===
*'''1a:''' "Metazoa" Taxonomy ID: 33208
Quite a lot extinct groups are encountered along the way - this is marked by a
*'''1b:''' Familiy containing humans: ''Hominidae''
small cross-shaped icon next to the group. Many of these groups do not have a
*'''1c:''' Yes, humans are certainly vertebrate (we have a spine), and that can been seen in the taxonomy by looking at the "full lineage" and seing we're members of the group "Vertebrata".
page dedicated to them but are there for putting the taxonomical placement of
modern groups into context.
A good example of an "important" extinct group which has a dedicated page is
"[http://www.tolweb.org/Ichthyostega/15015 Ichthyostega]", which was
one of the very first terrestrial vertebrates and had a lot of both "fish"
and "reptile" characteristics.
=== b) ===
7 species:
* ''Felis bieti'' (Chinese mountain cat)
* ''Felis catus'' (domestic cat)
* ''Felis chaus'' (jungle cat)
* ''Felis manul'' (Pallas' cat)
* ''Felis margarita'' (sand cat)
* ''Felis nigripes'' (black-footed cat)
* ''Felis silvestris'' (wildcat)
== Question 2:==
=== a) ===
Sus — this make perfect sense, since this is the "Genus" level and the Latin
name always consists of Genus + species: ''Sus scrofa''.
=== b)===
When we reach Artiodactyla (Danish: "Parrettåede hovdyr") other animals such as
camels, cows and hippos are included.
=== c)===
Artiodactyla (including the pigs) is the sister group to the Whales. The
interesting finding here is that the Whales branches off in the middle of the
mammalian tree — it's NOT an ancient branch after which the rest of the
mammals evolved. The whale group is only about 55 million years "old".
A lot of further information on the whale page:
http://tolweb.org/Cetacea/15977
 
==Question 3:==
=== a)===
Of the three main dinosaur groups Theropoda is NOT marked as extinct.
=== b)===
No - since extant ("still living") sub-groups exists.
=== c)===
Yes — all birds are descendants from the theropod dinosaurs and are therefore
dinosaurs in the taxonomical sense of the word.
Notice: The modern birds are a well defined taxonomical group (sharing a
single common ancestor) which can easily be separated from the rest of the
Dinosauria. The issue here is that it makes no sense to speak of Dinosauria
without including the birds - and the same way it wouldn't make sense to speak
of the mammals without including the pigs.
 
== Question 4:==
Taxonomy ID: 33208
 
== Question 5: ==
 
Hominidae


== Question 6: ==
== Question 2: ==


For both the Abbreviated and Full list:
Lowest ranking taxonomical group shared by Human (TaxID: 9606) and Mouse (TaxId:10090)


Euarchontoglires (rank: superorder) is the last common group before human and
*'''2a:''' (abbreviated lineage): '''Mammalia''' (rank: class) - Eng: Mammals
mouse branch off into primates and rodents.
*'''2b:''' (full lineage): '''Euarchontoglires''' (rank: superorder) is the last common group before human and mouse branch off into '''primates''' and '''rodents'''. This is a group of placental mammals.


== Question 7: ==
== Question 3: ==
Lowest ranking taxonomical group shared by Human (TaxID: 9606) and Fruit Fly (''D. melanogaster'' - TaxId:7227)


For both the Abbreviated and Full list:
*'''3a:''' (Abbreviated lineage): '''Metazoa''' (rank: kingdom) — this is the group of all animals.
*'''3b:''' (Full lineage): '''Bilateria''' (rank: clade (which just means a group) — sits between kingdom (Metazoa) and phylum (''Chordata'' for human, ''Arthropoda'' for the fly)).


Metazoa — "animals" (kingdom).
== Question 4: ==
 
== Question 8: ==


===a) ===
===a) ===
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https://www.sciencealert.com/actually-there-is-no-such-thing-as-a-fish-say-cladists
https://www.sciencealert.com/actually-there-is-no-such-thing-as-a-fish-say-cladists


== Question 9: ==
== Question 5: ==


===a) ===
===a) ===
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=== b) ===
=== b) ===
Yes, the trees can be made identical by swapping the Coelacanth and the lungfish.
Yes, the trees can be made identical by swapping the Coelacanth and the lungfish.
== Question 6: (AI assisted analysis) ==
No single answer can be given here - we'll discuss some example in class next week as part of the wrap-up.
In august 2026 a simple query Google AI with the question "''Does the category "fish" make any scientific sense? ''" gives a rather good overview explanation (see screenshot below).
'''NOTICE:''' It's clear that the AI has sourced (some of) the information from the Science Alert article we have also given as a reference under the answer to '''Q4f''' above.
[[Image:Taxonomy_AI_answer_2026.jpg|thumb|1000px|left]]
<br style="clear: both" />
------
We can ask the AI to dig deeper and add more scientific rigor by adding the prompt:
Follow up by expanding the answer with more scientific rigor.
Cite real scientific sources. This can both be scientific publications as well as
scientific reference databases (for example, but not limited to, NCBI Taxonomy).
This gives an answer broken down into the parts below. It is certainly possible to write it in a more concise manner, but it does capture the main points, and includes references beyond popular science articles and wikipedia. Notice that part 2 specifically talks about the distance in relationship between several of the brances of the tree we also have in our analysis (we use Cod, the analysis here uses Salmon as an example - both cases includes human and the lungfish).
[[Image:Taxonomy_AI_answer_2026_extA.jpg|frame|left]]
[[Image:Taxonomy_AI_answer_2026_extB.jpg|frame|left]]
[[Image: Taxonomy_AI_answer_2026_extC.jpg|frame|left]]

Latest revision as of 14:59, 28 August 2026

Answers to the Using the Taxonomy database exercise

Answers by: Rasmus Wernersson and Henrik Nielsen. Last update: Aug 2026

Question 1:

  • 1a: "Metazoa" Taxonomy ID: 33208
  • 1b: Familiy containing humans: Hominidae
  • 1c: Yes, humans are certainly vertebrate (we have a spine), and that can been seen in the taxonomy by looking at the "full lineage" and seing we're members of the group "Vertebrata".

Question 2:

Lowest ranking taxonomical group shared by Human (TaxID: 9606) and Mouse (TaxId:10090)

  • 2a: (abbreviated lineage): Mammalia (rank: class) - Eng: Mammals
  • 2b: (full lineage): Euarchontoglires (rank: superorder) is the last common group before human and mouse branch off into primates and rodents. This is a group of placental mammals.

Question 3:

Lowest ranking taxonomical group shared by Human (TaxID: 9606) and Fruit Fly (D. melanogaster - TaxId:7227)

  • 3a: (Abbreviated lineage): Metazoa (rank: kingdom) — this is the group of all animals.
  • 3b: (Full lineage): Bilateria (rank: clade (which just means a group) — sits between kingdom (Metazoa) and phylum (Chordata for human, Arthropoda for the fly)).

Question 4:

a)

The sister group to the Zebrafish is the cod.

The sister group to the lungfish is the Coelacanth (famous "Blue fish").

b)

Now, the sister group to the lungfish is you!

c)

you

d)

you

e)

you

f)

No! See https://www.sciencealert.com/actually-there-is-no-such-thing-as-a-fish-say-cladists

Question 5:

a)

Yes, there is a difference.

b)

Yes, the trees can be made identical by swapping the Coelacanth and the lungfish.

Question 6: (AI assisted analysis)

No single answer can be given here - we'll discuss some example in class next week as part of the wrap-up.

In august 2026 a simple query Google AI with the question "Does the category "fish" make any scientific sense? " gives a rather good overview explanation (see screenshot below).

NOTICE: It's clear that the AI has sourced (some of) the information from the Science Alert article we have also given as a reference under the answer to Q4f above.


We can ask the AI to dig deeper and add more scientific rigor by adding the prompt: 

Follow up by expanding the answer with more scientific rigor. 
Cite real scientific sources. This can both be scientific publications as well as 
scientific reference databases (for example, but not limited to, NCBI Taxonomy).

This gives an answer broken down into the parts below. It is certainly possible to write it in a more concise manner, but it does capture the main points, and includes references beyond popular science articles and wikipedia. Notice that part 2 specifically talks about the distance in relationship between several of the brances of the tree we also have in our analysis (we use Cod, the analysis here uses Salmon as an example - both cases includes human and the lungfish).

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