EvC Forum: Sequence comparisons (Bioinformatics?)

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Topic: Sequence comparisons (Bioinformatics?)

randman

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Message 6 of 42 (215543)
06-09-2005 1:14 AM

Reply to: Message 4 by MangyTiger
06-08-2005 11:17 PM

Re: An example from an absolute beginner

Dang. Good post there.

So we found one instance where the "pair" between the marsupial (golden mole) and the placental mole are more closely related (87%) than the 2 marsupial species of moles (83.3%) and the placental mole with the other Marsupial mole (83.6%). But it does seem a little bizzare.

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randman

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Message 13 of 42 (215748)
06-09-2005 8:46 PM

For many years their place within the Marsupials was hotly debated, some workers regarding it as an offshoot of the Diprotodontia (the order to which most living marsupials belong), others noting similarities to a variety of other creatures, and making suggestions that, in hindsight, appear bizarre. A 1989 review of the early literature, slightly paraphrased, states:

When Stirling (1888) initially was unable to find the epipubic bones in Marsupial Moles, speculation was rife: the Marsupial Mole was a monotreme, it was the link between monotremes and marsupials, it had it closest affinities with the (placental) golden moles, it was convergent with edentates, it was a polyprotodont diprotodont, and so on. [1] link
The mystery was not helped by the complete silence of the fossil record. On the basis that marsupial moles have some characteristics in common with almost all other marsupials, they were eventually classified as an entirely separate order: the Notoryctemorphia. Molecular level analysis in the early 1980s showed that the marsupial moles are not closely related to any of the living marsupials, and that they appear to have followed a separate line of development for a very long time, at least 50 million years.

Global Industry Market Sizing - NationMaster

The molecular data given here does not seem to match what we have come up with in our scant review. Maybe the Marsupial mole is worth looking into a bit more?

Note also that prior to the molecular data, there were anatomists that speculated:

it had it closest affinities with the (placental) golden moles

This message has been edited by randman, 06-09-2005 08:47 PM

edited by AdminJar to shorten link.

This message has been edited by AdminJar, 06-10-2005 12:20 PM

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randman

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Message 15 of 42 (215897)
06-10-2005 1:13 PM

Reply to: Message 14 by Wounded King
06-10-2005 6:13 AM

WK, I am not saying encyclopedia articles are correct, but they usually tell you what the majority academic opinion is.

To me, it's useful to see that. Obviously I don't always agree with it, but it sheds light on what the experts in that field are thinking. Unfortnately, experts in the field can still be, and are often, wrong.

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Message 17 of 42 (216062)
06-11-2005 2:26 AM

Reply to: Message 16 by Entomologista
06-11-2005 12:13 AM

Turtle, Kangaroo, and Rattlesnake

This is what I got for CytoC comparisons for turtle, kangaroo and rattlesnake.

{qs Sequence 1: TurtleCytC>GDVEKGKKIFVQKCAQCHT 34 aa
Sequence 2: KangarooCytC>GDVEKGKKIFVQKCAQC 34 aa
Sequence 3: RattlesnaleCytC>GDVEKGKKIFSMKC 34 aa
Start of Pairwise alignments
Aligning...

Sequences (1:2) Aligned. Score: 88.2353
Sequences (1:3) Aligned. Score: 76.4706
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 73.5294
Sequences (3:2) Aligned. Score: 73.5294
Sequences (3:3) Aligned. Score: 100 [/qs]

This suggests that the kangaroo and the turtle are more closely related than the turtle and rattlesnake, but that's not what current phylogenies would predict.

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Message 18 of 42 (216063)
06-11-2005 2:40 AM

Reply to: Message 17 by randman
06-11-2005 2:26 AM

Re: Turtle, Kangaroo, and Rattlesnake

Also, with humans added. People are more related to rattlesnakes than kangaroos.....hmmm.

Sequence 1: TurtleCytC>GDVEKGKKIFVQKCAQCHT 34 aa
Sequence 2: KangarooCytC>GDVEKGKKIFVQKCAQC 34 aa
Sequence 3: RattlesnaleCytC>GDVEKGKKIFSMKC 34 aa
Sequence 4: humancytoC>MPSTLPAPRRTHAARTASL 378 aa
Start of Pairwise alignments
Aligning...

Sequences (1:2) Aligned. Score: 88.2353
Sequences (1:3) Aligned. Score: 76.4706
Sequences (1:4) Aligned. Score: 20.5882
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 73.5294
Sequences (2:4) Aligned. Score: 17.6471
Sequences (3:2) Aligned. Score: 73.5294
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 23.5294
Sequences (4:2) Aligned. Score: 17.6471
Sequences (4:3) Aligned. Score: 23.5294
Sequences (4:4) Aligned. Score: 100

This message has been edited by randman, 06-11-2005 02:41 AM

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randman

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Message 19 of 42 (216064)
06-11-2005 2:48 AM

here's one with CytoB

It still doesn't match with current hypotheses.

It looks like the site will give you wrong data for common names. I looked up and ran the scientific names though, and got the following. Please note that "alligator" is alligator snapping turtle, aka Macroclemys temminckii.

Sequence 1: humanCytoB>MTPMRKINPLMKLINHSFI 308 aa
Sequence 2: rattlesnakeCytoB>MMQTMTGFFLAIH 155 aa
Sequence 3: redkangaroo>MTNLRKTHPLIKIVNHSF 311 aa
Sequence 4: alligator 198 aa
Start of Pairwise alignments
Aligning...

Sequences (1:2) Aligned. Score: 58.7097
Sequences (1:3) Aligned. Score: 75.6494
Sequences (1:4) Aligned. Score: 77.7778
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 61.2903
Sequences (2:4) Aligned. Score: 62.5806
Sequences (3:2) Aligned. Score: 61.2903
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 77.2727
Sequences (4:2) Aligned. Score: 62.5806
Sequences (4:3) Aligned. Score: 77.2727
Sequences (4:4) Aligned. Score: 100
_{>humanCytoB>MTPMRKINPLMKLINHSFIDLPTPSNISAWWNF
GSLLGACLILQITTGLFLAMHYSPDASTAFSSIAHIT
RDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFL
YSETWNIGIILLLATMATAFMGYVLPWGQMSF
WGATVITNLLSAIPYIGTDLVQWIWGGYSVDSPTLTRFF
TFHFILPFIIAALAALHLLFLHETGSNNPLG
ITSHSDKITFHPYYTIKDALGLLLFLLSLMTLTLFSPDLLGDPDN
YTLANPLNTPPHIKPEWYFLFAYTI
LRSVPNKLGGVLALLLSILILAMIPILHMSKQQSMMF
RPLSQSLYWLLAADLLILTWIGGQPVSYPFTII
GQVASVLYFTTILILMPTISLIENKMLK
>rattlesnakeCytoB>MMQTMTGFFLAIHYTANINLAFSSVIHITRDVPYGXIMQNLHTISASL
FFICIYIHIARGLYYGLYLNKE
VWLSGTALLITLMATAFFGYVLPWGQMSFWAATVITNLLTAIPYLGTTLTTWL
WGGFSINDPTLTRFFAL
HFILPFIIISLSSIHIILLHNEGSNNPLGTNSDIDKIPFHPYHS
YKDVLMITSMITLLLLILSFSPSLLN
DPENFXKAXPXXTPQ
>redkangaroo>MTNLRKTHPLIKIVNHSFIDLPAPSNISAWWNF
GSLLGACLIIQILTGLFLAMHYTADTLTAFSSVAHIC
RDVNYGWLIRNLHANGASMFFMCLFLHVGRGIYYGSYLYKETW
NIGVILLLTVMATAFVGYVLPWGQMSF
WGATVITNLLSAIPYIGTTLVEWIWGGFSVDKATLTRFFAFHF
ILPFIITALVLVHLLFLHETGSNNPSG
INPDSDKIPFHPYYTIKDALGFMLMLLILLTLALFSPDML
GDPDNFSPAKPTEHSSHIKPEWYFLFAYAI
LRSIPNKLGGVLALLASILILLIIPLLHTSKQRSLMFRPISQTLF
WILTANLITLTWIGGQPVEQPYIII
GQVASISYFLLIIVLMPLAGLFENYMLEPKW
>alligator snapping turlte>MATNLRKTHPMMKIINNSFIDLPSPSNISAWWNFGSLLGTCLI
MQTITGIFLAMHYSPDISMAFSSITHI
TRDVQYGWLIRNMHANGASLFFICIYLHIGRGLYYGSYL
YKETWNTGVILLLLTMATAFMGYVLPWGQMS
FWGATVITNLLSAIPYIGSTLVQWIWGGFSVDNATLTRFFTLHFLLPFTIMG
LAMVHLLFLHETGSNNPT
GLNSNSDKIPFHPYFSYKDLLGLILMLSLLLTLALFSPNLLGDPDNFTPANPLVTPPH}

Humans are more related to alligator snapping turtles than a red kangaroo, aka Macropus rufus?

This message has been edited by randman, 06-11-2005 03:28 AM

This message has been edited by AdminJar, 06-12-2005 10:56 AM

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randman

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Message 20 of 42 (216080)
06-11-2005 4:02 AM

Cyto B comparisons for a mouse, human, red wolf, and alligator snapping turtle.

Sequence 1: MusmusculusCytoB>MGDWAVNEGLSIF 500 aa
Sequence 2: humanCytoB>MTPMRKINPLMKLINHSFI 308 aa
Sequence 3: MacropusrufusCytB>MTNLRKTHPLIK 311 aa
Sequence 4: Macroclemys 198 aa
Start of Pairwise alignments
Aligning...

Sequences (1:2) Aligned. Score: 11.039
Sequences (1:3) Aligned. Score: 11.8971
Sequences (1:4) Aligned. Score: 12.1212
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 75.6494
Sequences (2:4) Aligned. Score: 77.7778
Sequences (3:2) Aligned. Score: 75.6494
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 77.2727
Sequences (4:2) Aligned. Score: 77.7778
Sequences (4:3) Aligned. Score: 77.2727
Sequences (4:4) Aligned. Score: 100

randman

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Message 27 of 42 (216220)
06-11-2005 5:24 PM

Reply to: Message 26 by Modulous
06-11-2005 9:02 AM

Re: here's one with CytoB

Modulous, I don't doubt we are making mistakes, as WK, pointed out, but it seems the data is getting fairly consistent in placing turtles way too close to us compared to kangaroos, another mammal.

74 and 76 are nearly identical in some respects.

I have to be honest and state I chose the turtle, rattlesnake, humans, and kangaroo because I read somewhere the data did not fit. I am probably not even a "keen amatuer" when it comes to DNA, but the creationist that made that comment was correct, it seems.

Not sure what this means just yet though. I suspect we will have a better picture in a few years.

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