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Author | Topic: Sequence comparisons (Bioinformatics?) | |||||||||||||||||||||||
randman  Suspended Member (Idle past 4925 days) Posts: 6367 Joined: |
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  Suspended Member (Idle past 4925 days) Posts: 6367 Joined: |
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] linkThe 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  Suspended Member (Idle past 4925 days) Posts: 6367 Joined: |
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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randman  Suspended Member (Idle past 4925 days) Posts: 6367 Joined: |
This is what I got for CytoC comparisons for turtle, kangaroo and rattlesnake.
{qs Sequence 1: TurtleCytC>GDVEKGKKIFVQKCAQCHT 34 aaSequence 2: KangarooCytC>GDVEKGKKIFVQKCAQC 34 aa Sequence 3: RattlesnaleCytC>GDVEKGKKIFSMKC 34 aa Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 88.2353Sequences (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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randman  Suspended Member (Idle past 4925 days) Posts: 6367 Joined: |
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: 88.2353Sequences (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  Suspended Member (Idle past 4925 days) Posts: 6367 Joined: |
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: 58.7097Sequences (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>MMQTMTGFFLAIHYTANINLAFSSVIHITRDVPYGXIMQNLHTISASLFFICIYIHIARGLYYGLYLNKE VWLSGTALLITLMATAFFGYVLPWGQMSFWAATVITNLLTAIPYLGTTLTTWL WGGFSINDPTLTRFFAL HFILPFIIISLSSIHIILLHNEGSNNPLGTNSDIDKIPFHPYHS YKDVLMITSMITLLLLILSFSPSLLN DPENFXKAXPXXTPQ >redkangaroo>MTNLRKTHPLIKIVNHSFIDLPAPSNISAWWNFGSLLGACLIIQILTGLFLAMHYTADTLTAFSSVAHIC RDVNYGWLIRNLHANGASMFFMCLFLHVGRGIYYGSYLYKETW NIGVILLLTVMATAFVGYVLPWGQMSF WGATVITNLLSAIPYIGTTLVEWIWGGFSVDKATLTRFFAFHF ILPFIITALVLVHLLFLHETGSNNPSG INPDSDKIPFHPYYTIKDALGFMLMLLILLTLALFSPDML GDPDNFSPAKPTEHSSHIKPEWYFLFAYAI LRSIPNKLGGVLALLASILILLIIPLLHTSKQRSLMFRPISQTLF WILTANLITLTWIGGQPVEQPYIII GQVASISYFLLIIVLMPLAGLFENYMLEPKW >alligator snapping turlte>MATNLRKTHPMMKIINNSFIDLPSPSNISAWWNFGSLLGTCLIMQTITGIFLAMHYSPDISMAFSSITHI 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  Suspended Member (Idle past 4925 days) Posts: 6367 Joined: |
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: 11.039Sequences (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 |
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randman  Suspended Member (Idle past 4925 days) Posts: 6367 Joined: |
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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