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:
I would expect (he says sticking his neck out way beyond his knowledge!) that the marsupial mole is genetically much more similar to another marsupial - probably any marsupial - than it is to the placental mole.
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:
>Marsupial Mole Cytochrome b
MVNLRKTHPLMKIINHSFIDLPAPSNISAWWNFGSLLGICLIIQILTGLFLAMHYTSDTYTAFSSVAHIC
RDVNYGWLIRNLHANGASMFFMCLFLHVGRGIYYGSYLYKETWNIGVILLLTVMATAFVGYVLPWGQMSF
WGATVITNLLSAIPYIGTTLVEWIWGGFSVDKATLTRFFAFHFILPFIIAALAIVHLIFLHETGSNNPSG
INPDADKIPFHPYYTIKDALGLLFLLLLLLSLALFSPDLLGDPDNFSPANPLNTPPHIKPEWYFLFAYAI
LRSIPNKLGGVLALLASIMILLIIPLLHTSNQRSMTFRPISQILYWILAANLLVLTWIGGQPVEQPFIII
GQLASILYFLLIILLMPLAGLFENYMLEPKW
>Cape Golden Mole Cytochrome b
MTNIRKTHPLLKIINHSFIDLPAPSNISAWWNFGSLLGLCLIIQILTGLFLAMHYTSDTSTAFSSVTHIC
RDVNNGWLIRYLHANGASMFFICLFTHVGRGIYYGSYLFLETWNIGIILLFAVMATAFMGYVLPWGQMSF
WGATVITNLLSAIPYIGTTLVEWIWGGFSVDKATLTRFFAFHFILPFIVAALTMVHLLFLHETGSNNPSG
LNSDADKIPFHPYYTVKDLLGVLMLLLFLLLLTLFSPDLLGDPDNYIPANPLNTPPHIKPEWYFLFAYAI
LRSIPNKLGGVLALVFSILILAAFPLLHMSHQRSLMFRPLSQCMFWILVADLFTLTWIGGQPVEHPFIII
GQLASILYFTIILVLMPVSSMIENRLLKW
>European Mole Cytochrome b
MTNIRKTHPLMKIVNSSFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTMTAFSSVTHIC
RDVNYGWLIRYLHANGASMFFICLFLHVGRGLYYGSYMFMETWNIGVLLLFAVMATAFMGYVLPWGQMSF
WGATVITNLLSAIPYIGTDLVEWIWGGFSVDKATLTRFFAFHFILPFIIAALAGVHLLFLHETGSNNPSG
LSSDTDKIPFHPYYTIKDILGALILIMALSSLVLFSPDLLGDPDNYIPANPLNTPPHIKPEWYFLFAYAI
LRSIPNKLGGVLALVFSILVLALMPFLHTSKQRSMMFRPISQCLFWLLVADLFTLTWIGGQPVEHPFIII
GQLASILYFALILMLMPLASLMENNLLKW
>Giraffe Cytochrome b
MINIRKSHPLMKIVNNALIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTPDTTTAFSSVTHIC
RDVNYGWIIRYMHANGASMFFICLFMHVGRGLYYGSYTFLETWNIGVILLFTVMATAFMEYVLPWGQMSF
WGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFAFHFILPFIIMALTMVHLLFLHETGSNNPMG
IPSDMDKIPFHPYYTIKDILGALLLILVLMLLVLFTPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAI
LRSIPNKLGGVLALVLSILILIFMPLLHTSKQRSMMFRPFSQCLFWILVADLLTLTWIGGQPVEHPFIII
GQLASIMYFLIILVLMPVTSAIQNNLLKW
>Thylacine Cytochrome b
MIIMRKTHPLLKTINHSFIDLPAPSNISAWWNFGSLLGICLVIQILTGLFLAMHYTSDTSTAFSSVAHIC
RDVNYGWLIRNLHANGASMFFMCLFLHVGRGIYYGSYLYKETWNIGVILLLTVMATAFVGYVLPWGQMSF
WGATVITNLLSAIPYIGTTLAEWVWGGFAVDKATLTRFFAFHFILPSIVTARATVHLLFLHETGSNNPSG
INPDSDKIPFHPYYTIKDALGLMLLLLPLLPLALFSPDLLGDPDNFSPANPLNTPPHIKPEWYFLFAYAI
LRSIPNKLGGVLALLASILILLIIPLLHTSNQRSMMFRPISQTLFWILAANLLTLTWIGGQPVEQPFIII
GQLAIILYFLLIVVLMPLAGLLENYMLEPKW
I then put these into CLUSTALW and got these results:
Sequence type explicitly set to Protein
Sequence format is Pearson
Sequence 1: Marsupial 381 aa
Sequence 2: Cape 379 aa
Sequence 3: European 379 aa
Sequence 4: Giraffe 379 aa
Sequence 5: Thylacine 381 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 83.3773
Sequences (1:3) Aligned. Score: 83.6412
Sequences (1:4) Aligned. Score: 80.7388
Sequences (1:5) Aligned. Score: 92.126
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 87.3351
Sequences (2:4) Aligned. Score: 85.752
Sequences (2:5) Aligned. Score: 82.5858
Sequences (3:2) Aligned. Score: 87.3351
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 87.5989
Sequences (3:5) Aligned. Score: 81.2665
Sequences (4:2) Aligned. Score: 85.752
Sequences (4:3) Aligned. Score: 87.5989
Sequences (4:4) Aligned. Score: 100
Sequences (4:5) Aligned. Score: 79.6834
Sequences (5:2) Aligned. Score: 82.5858
Sequences (5:3) Aligned. Score: 81.2665
Sequences (5:4) Aligned. Score: 79.6834
Sequences (5:5) Aligned. Score: 100
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: 79.6834
This 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!
Oops! Wrong Planet