Sequence comparisons (Bioinformatics?)

I decided to have a go at this.In Message 301 (one of the last messages in the precursor thread to the one Ned referenced in the OP) I talked about the external similarities of the marsupial and placental mole. I also made this prediction: With all the info WK has posted (and I think we should all offer him our thanks for showing us this great new toy ) I figured I could actually test out my prediction, and I offer up my attempt for WK or any other expert to point out if I've screwed up or to comment on my results.There is one very strange thing that makes me wonder if I messed something up - more on that later.First the animals I picked. Obviously there is are the placental and marsupial moles, then I needed another marsupial to compare against and although not included in my prediction I decided to include another placental mammal. This was because I expected the two placentals to be closer to each other than to either of the marsupials.Since this was all about convergent evolution (the two moles) I wanted to pick the other animals to be fairly different from moles. For the marsupial I picked our old friend the thylacine and for the placental I picked the giraffe - both quite different to moles I think you'll agree!While investigating placental moles I discovered there are lots of them. The one which seems to most closely resemble the marsupial mole is one of the golden moles - I went for the Cape golden mole. For good measure I also threw in the European mole.So I ended up with this list (I got the Latin names from Googling):

• Marsupial Mole (Notoryctes typhlops)
• Cape Golden Mole (Chrysochloris asiatica)
• European Mole (Calcochloris obtusirostris)
• Giraffe (Giraffa camelopardalis)
• Thylacine (Thylacinus cynocephalus)

Using Entrez I got the following results for Cytochrome b: I then put these into CLUSTALW and got these results: The N-J tree splits off the two marsupials like you would expect but threw a bit of a curve ball with the placentals.It actually has the giraffe and the European mole having a common ancestor after the common ancestor they both shared with the Cape golden mole.Since I can't host images the best way I can show it is to arrange the results table from CLUSTALW in descending order:Sequences (1:5) Aligned. Score: 92.126
Sequences (3:4) Aligned. Score: 87.5989
Sequences (2:3) Aligned. Score: 87.3351
Sequences (2:4) Aligned. Score: 85.752
Sequences (1:3) Aligned. Score: 83.6412
Sequences (1:2) Aligned. Score: 83.3773
Sequences (2:5) Aligned. Score: 82.5858
Sequences (3:5) Aligned. Score: 81.2665
Sequences (1:4) Aligned. Score: 80.7388
Sequences (4:5) Aligned. Score: 79.6834This shows the two most closely related are 1 and 5 (Marsupial Mole and Thylacine), but the second most closely related are 3 and 4 (European Mole and Giraffe). I would have expected the two placental moles to be more closely related to each other than either of them are to the giraffe.Maybe this is just an artifact of not having enough data sets?Ot maybe I've got it all completely wrong!

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Oops! Wrong Planet

Bioinformatics?Sounds like something you can order from an Amazing Discoveries infomercial

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Oops! Wrong Planet

No no no!The golden mole is another variant of placental mole. Here are the five animals:

1. Marsupial Mole (Notoryctes typhlops)
2. Cape Golden Mole (Chrysochloris asiatica)
3. European Mole (Calcochloris obtusirostris)
4. Giraffe (Giraffa camelopardalis)
5. Thylacine (Thylacinus cynocephalus)

The marsupials are numbers 1 and 5.The similarity scores with the animal names added are:Sequences (1:5) Aligned. Score: 92.126 (Marsupial Mole:Thylacine)
Sequences (3:4) Aligned. Score: 87.5989 (European Mole:Giraffe)
Sequences (2:3) Aligned. Score: 87.3351 (Cape Golden Mole:European Mole)
Sequences (2:4) Aligned. Score: 85.752 (Cape Golden Mole:Giraffe)
Sequences (1:3) Aligned. Score: 83.6412 (Marsupial Mole:European Mole)
Sequences (1:2) Aligned. Score: 83.3773 (Marsupial Mole:Cape Golden Mole)
Sequences (2:5) Aligned. Score: 82.5858 (Cape Golden Mole:Thylacine)
Sequences (3:5) Aligned. Score: 81.2665 (European Mole:Thylacine)
Sequences (1:4) Aligned. Score: 80.7388 (Marsupial Mole:Giraffe)
Sequences (4:5) Aligned. Score: 79.6834 (Giraffe:Thylacine)So the most similar animals are the Marsupial mole and Thylacine (the Tasmanian wolf remember). The second third and fourth closest relationships are between the three placental animals and the remaining values are for the various permutations of one placental and one marsupial.Note that this indicates that the two kinds of placental mole are both more closely related to the giraffe than they are to the marsupial mole.The only odd thing is that the European mole appears to be more closely related to the giraffe than it does to the Cape golden mole - everything else is in line with what I predicted.

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Oops! Wrong Planet

Now that's a cool tree I'm going in to hospital on Friday morning for a few days but when I get back I'm going to have a go and see if I can produce something like it and then extend it to include the moles and giraffe from the example I posted earlier (and maybe a mole-rat as well).This is mostly just for my own entertainment but also because the result I got where a giraffe shows as more more closely related to one placental mole than that mole was with a different placental mole is bugging me!

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Oops! Wrong Planet