>Tyrannosaurus_rex GLPGESGAVGPAGPIGSR >Homo_sapiens MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPAGDRGPRGERGPPGPPGRDGEDGPTGPPGPPGPPGP PGLGGNFAAQYDGKGVGLGPGPMGLMGPRGPPGAAGAPGPQGFQGPAGEPGEPGQTGPAGARGPAGPPGK AGEDGHPGKPGRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGAPGVKGEPGAPGENGTP GQTGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGPPGFPGAPGPKGEIGAVGNAGPAGPAG PRGEVGLPGLSGPVGPPGNPGANGLTGAKGAAGLPGVAGAPGLPGPRGIPGPVGAAGATGARGLVGEPGP AGSKGESGNKGEPGSAGPQGPPGPSGEEGKRGPNGEAGSAGPPGPPGLRGSPGSRGLPGADGRAGVMGPP GSRGASGPAGVRGPNGDAGRPGEPGLMGPRGLPGSPGNIGPAGKEGPVGLPGIDGRPGPIGPAGARGEPG NIGFPGPKGPTGDPGKNGDKGHAGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPPGPPGFQGLPGP SGPAGEVGKPGERGLHGEFGLPGPAGPRGERGPPGESGAAGPTGPIGSRGPSGPPGPDGNKGEPGVVGAV GTAGPSGPSGLPGERGAAGIPGGKGEKGEPGLRGEIGNPGRDGARGAPGAVGAPGPAGATGDRGEAGAAG PAGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGAKGERGAKGPKGENGVVGPTGPVGAAGPAGPNGP PGPAGSRGDGGPPGMTGFPGAAGRTGPPGPSGISGPPGPPGPAGKEGLRGPRGDQGPVGRTGEVGAVGPP GFAGEKGPSGEAGTAGPPGTPGPQGLLGAPGILGLPGSRGERGLPGVAGAVGEPGPLGIAGPPGARGPPG AVGSPGVNGAPGEAGRDGNPGNDGPPGRDGQPGHKGERGYPGNIGPVGAAGAPGPHGPVGPAGKHGNRGE TGPSGPVGPAGAVGPRGPSGPQGIRGDKGEPGEKGPRGLPGLKGHNGLQGLPGIAGHHGDQGAPGSVGPA GPRGPAGPSGPAGKDGRTGHPGTVGPAGIRGPQGHQGPAGPPGPPGPPGPPGVSGGGYDFGYDGDFYRAD QPRSAPSLRPKDYEVDATLKSLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDA IKVYCDFSTGETCIRAQPENIPAKNWYRSSKDKKHVWLGETINAGSQFEYNVEGVTSKEMATQLAFMRLL ANYASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKKTNEWGKTIIE YKTNKPSRLPFLDIAPLDIGGADQEFFVDIGPVCFK >Gallus_gallus MLSFVDTRILLLLAVTSYLATSQHVSEASAGRKGPRGDKGPQGERGPPGPPGRDGEDGPPGPPGPPGPPG LGGNFAAQYDPSKAADFGPGPMGLMGPRGPPGASGPPGPPGFQGVPGEPGEPGQTGPQGPRGPPGPPGKA GEDGHPGKPGRPGERGVAGPQGARGFPGTPGLPGFKGIRGHNGLDGQKGQPGTPGTKGEPGAPGENGTPG QPGARGLPGERGRIGAPGPAGARGSDGSAGPTGPAGPIGAAGPPGFPGAPGAKGEIGPAGNVGPTGPAGP RGEIGLPGSSGPVGPPGNPGANGLPGAKGAAGLPGVAGAPGLPGPRGIPGPPGPAGPSGARGLVGEPGPA GAKGESGNKGEPGAAGPPGPPGPSGEEGKRGSNGEPGSAGPPGPAGLRGVPGSRGLPGADGRAGVMGPAG NRGASGPVGAKGPNGDAGRPGEPGLMGPRGLPGQPGSPGPAGKEGPVGFPGADGRVGPIGPAGNRGEPGN IGFPGPKGPTGEPGKPGEKGNVGLAGPRGAPGPEGNNGAQGPPGVTGNQGAKGETGPAGPPGFQGLPGPS GPAGEAGKPGERGLHGEFGVPGPAGPRGERGLPGESGAVGPAGPIGSRGPSGPPGPDGNKGEPGNVGPAG APGPAGPGGIPGERGVAGVPGGKGEKGAPGLRGDTGATGRDGARGLPGAIGAPGPAGGAGDRGEGGPAGP AGPAGARGIPGERGEPGPVGPSGFAGPPGAAGQPGAKGERGPKGPKGETGPTGAIGPIGASGPPGPVGAA GPAGPRGDAGPPGMTGFPGAAGRVGPPGPAGITGPPGPPGPAGKDGPRGLRGDVGPVGRTGEQGIAGPPG FAGEKGPSGEAGAAGPPGTPGPQGILGAPGILGLPGSRGERGLPGIAGATGEPGPLGVSGPPGARGPSGP VGSPGPNGAPGEAGRDGNPGNDGPPGRDGAPGFKGERGAPGNPGPSGALGAPGPHGQVGPSGKPGNRGDP GPVGPVGPAGAFGPRGLAGPQGPRGEKGEPGDKGHRGLPGLKGHNGLQGLPGLAGQHGDQGPPGNNGPAG PRGPPGPSGPPGKDGRNGLPGPIGPAGVRGSHGSQGPAGPPGPPGPPGPPGPNGGGYEVGFDAEYYRADQ PSLRPKDYEVDATLKTLNNQIETLLTPEGSKKNPARTCRDLRLSHPEWSSGFYWIDPNQGCTADAIRAYC DFATGETCIHASLEDIPTKTWYVSKNPKDKKHIWFGETINGGTQFEYNGEGVTTKDMATQLAFMRLLANH ASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVELRAEGNSRFTFSVLVDGCSKKNNKWGKTIIEYRT NKPSRLPILDIAPLDIGGADQEFGLHIGPVCFK >Rattus_norvegicus MLSFVDTRTLLLLAVTSCLATCQSLQMGSVRKGPTGDRGPRGQRGPAGPRGRDGVDGPVGPPGPPGAPGP PGPPGPPGLTGNFAAQYSDKGVSAGPGPMGLMGPRGPPGAVGAPGPQGFQGPAGEPGEPGQTGPAGSRGP AGPPGKAGEDGHPGKPGRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGAQGVKGEPGAP GENGTPGQAGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGPPGFPGAPGPKGELGPVGNPG PAGPAGPRGEAGLPGLSGPVGPPGNPGANGLTGAKGATGLPGVAGAPGLPGPRGIPGPVGAAGATGPRGL VGEPGPAGSKGETGNKGEPGSAGAQGPPGPSGEEGKRGSPGEPGSAGPAGPPGLRGSPGSRGLPGADGRA GVMGPPGNRGSTGPAGVRGPNGDAGRPGEPGLMGPRGLPGSPGNVGPAGKEGPVGLPGIDGRPGPIGPAG PRGEAGNIGFPGPKGPSGDPGKPGEKGHPGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAGPPGF QGLPGPSGTAGEVGKPGERGLPGEFGLPGPAGPRGERGPPGESGAAGPSGPIGSRGPSGAPGPDGNKGEA GAVGAPGSAGASGPGGLPGERGAAGIPGGKGEKGETGLRGEIGNPGRDGARGAPGAIGAPGPAGASGDRG EAGAAGPSGPAGPRGSPGERGEVGPAGPNGFAGPAGSAGQPGAKGEKGTKGPKGENGIVGPTGPVGAAGP SGPNGPPGPAGSRGDGGPPGMTGFPGAAGRTGPPGPSGITGPPGPPGAAGKEGIRGPRGDQGPVGRTGEI GASGPPGFAGEKGPSGEPGTTGPPGTAGPQGLLGAPGILGLPGSRGERGLPGIAGALGEPGPLGIAGPPG ARGPPGAVGSPGVNGAPGEAGRDGNPGSDGPPGRDGQPGHKGERGYPGNIGPTGAAGAPGPHGSVGPAGK HGNRGEPGPAGSVGPVGAVGPRGPSGPQGIRGDKGEPGDKGARGLPGLKGHNGLQGLPGLAGLHGDQGAP GPVGPAGPRGPAGPSGPIGKDGRSGHPGPVGPAGVRGSQGSQGPAGPPGPPGPPGPPGVSGGGYDFGFEG DFYRADQPRSQPSLRPKDYEVDATLKSLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWKSDYYWIDPNQ GCTMDAIKVYCDFSTGETCIQAQPVNTPAKNAYSRAQANKHVWLGETINGGSQFEYNAEGVSSKEMATQL AFMRLLANRASQNITYHCKNSIAYLDEETGRLNKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKKTNEW DKTIIEYKTNKPSRLPFLDIAPLDIGGTNQEFRVEVGPVCFK >Mus_musculus MLSFVDTRTLLLLAVTSCLATCQYLQSGSVRKGPTGDRGPRGQRGPAGPRGRDGVDGPMGPPGPPGSPGP PGSPAPPGLTGNFAAQYSDKGVSSGPGPMGLMGPRGPPGAVGAPGPQGFQGPAGEPGEPGQTGPAGPRGP AGSPGKAGEDGHPGKPGRPGERGVVGPQGARGFPGTPGLPGFKGVKGHSGMDGLKGQPGAQGVKGEPGAP GENGTPGQAGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGPPGFPGAPGPKGELGPVGNPG PAGPAGPRGEVGLPGLSGPVGPPGNPGTNGLTGAKGATGLPGVAGAPGLPGPRGIPGPAGAAGATGARGL VGEPGPAGSKGESGNKGEPGSVGAQGPPGPSGEEGKRGSPGEAGSAGPAGPPGLRGSPGSRGLPGADGRA GVMGPPGNRGSTGPAGIRGPNGDAGRPGEPGLMGPRGLPGSPGNVGPSGKEGPVGLPGIDGRPGPIGPAG PRGEAGNIGFPGPKGPSGDPGKPGERGHPGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAGPPGF QGLPGPSGTTGEVGKPGERGLPGEFGLPGPAGPRGERGTPGESGAAGPSGPIGSRGPSGAPGPDGNKGEA GAVGAPGSAGASGPGGLPGERGAAGIPGGKGEKGETGLRGDTGNTGRDGARGIPGAVGAPGPAGASGDRG EAGAAGPSGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGAKGEKGTKGPKGENGIVGPTGSVGAAGP SGPNGPPGPVGSRGDGGPPGMTGFPGAAGRTGPPGPSGIAGPPGPPGAAGKEGIRGPRGDQGPVGRTGET GASGPPGFVGEKGPSGEPGTAGAPGTAGPQGLLGAPGILGLPGSRGERGLPGIAGALGEPGPLGISGPPG ARGPPGAVGSPGVNGAPGEAGRDGNPGSDGPPGRDGQPGHKGERGYPGSIGPTGAAGAPGPHGSVGPAGK HGNRGEPGPAGSVGPVGAVGPRGPSGPQGIRGDKGEPGDKGHRGLPGLKGYSGLQGLPGLAGLHGDQGAP GPVGPAGPRGPAGPSGPVGKDGRSGQPGPVGPAGVRGSQGSQGPAGPPGPPGPPGPPGVSGGGYDFGFEG DFYRADQPRSQPSLRPKDYEVDATLKSLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWNSDYYWIDPNQ GCTMDAIKVYCDFSTGETCIQAQPVNTPAKNSYSRAQANKHVWLGETINGGSQFEYNVEGVSSKEMATQL AFMRLLANRASQNITYHCKNSIAYLDEETGSLNKAVLLQGSNDVELVAEGNSRFTYSVLVDGCSKKTNEW GKTIIEYKTNKPSRLPFLDIAPLDIGGADQEFRVEVGPVCFK >Danio_rerio MLSFVDTRILLLLAVTSYLASCQSGLKGPKGPRGERGPKGPDGKPGRPGLPGPAGPPGPPGLGGNFAAQY DGAKGPDPGPGPMGLMGPRGPSGSPGAPGAQGLQGHAGEPGEPGQAGAIGARGPPGPPGKNGEDGNNGRP GKPGDRGVLGAQGARGFPGTPGLPGMKGHRGYNGIDGRKGEPGAAGAKGENGAAGSNGTPGQRGGRGLPG ERGRVGPAGPAGARGADGNTGPAGPAGPLGSAGPPGFPGAPGPKGELGPAGPTGPSGAQGQRGEPGPNGA VGPVGPPGNPGANGINGAKGAAGLPGIAGAPGFPGPRGGPGPQGPSGASGPRGLGGDPGPVGVKGDSGVK GEPGSAGPQGPPGPSGEEGKRGSTGEQGPTGPLGLRGPRGAAGTRGLPGLAGRSGPMGMPGPRGGVGAPG ARGPPGDAGRAGEAGLVGARGLPGSPGSSGPPGKEGPSGAAGQDGRTGPPGPTGPRGQPGNIGFPGPKGP SGEAGKPGEKGPVGPTGLRGSPGPDGNNGPAGPVGLAGAPGEKGEQGPSGAPGFQGLPGPAGPVGEAGKP GDRGIPGDQGVSGPAGVKGERGNPGPAGAAGAQGPIGARGPSGTPGPDGNKGEPGAVGPAGAPGPQGAAG MPGERGAAGTPGAKGEKGEAGYRGLEGNAGKDGARGAPGPSGPPGPAGANGDKGETGSFGPPGPAGPRGA PGERGESGPAGPSGFAGPPGADGQTGPRGEKGPAGGKGDAGPAGPAGPAGNTGPLGPSGPVGPPGARGDS GPTGLTGFPGAPGRVGPPGPAGIVGPAGLTGPAGKDGPRGPRGDVGPAGPPGENGMIGPLGLAGEKGPPG EAGAPGAPGPAGPQGQLGSQGFNGLPGSRGDRGLPGIPGSVGEPGRVGPAGAPGARGPGGNIGMPGMTGP QGEAGREGSPGNDGPPGRPGAAGIKGDRGEPGSPGTAGPVGAPGPNGPSGAVGRPGNRGESGPSGPTGAV GPAGARGAPGPAGPRGEKGVAGEKGDRGMKGLRGHPGLQGMPGPNGPSGDSGPAGIAGPSGPRGPAGPNG PAGKDGSNGMPGAIGPPGHRGPAGHVGPAGPPGSPGLPGPPGPSGGGYDTSGGYDEYRADQASLRAKDYE VDATIKSLNTQIENLLSPEGSKKNPARTCRDIRLSHPEWSSGFYWIDPNQGCTMDAIKAFCDFSTGQTCI HPHPESIPRKNWYRSSQEKKHTWFGETINSGTEFAYNDETLSPQSMATQLAFMRLLANQAVQNITYHCKN SIAYMDAENGNLKKAVLLQGSNDVELRAEGNSRFTFSVLEDGCSRHTGQWSKTVIEYRTNKPSRLPILDI APLDIGGADQEFGLDIGPVCFK
Tree of Life Activity Part 5
The living relatives of Tyrannosaurus rex
Images from Smithsonian Insider and Smithsonian magazine
Scientists have observed that dinosaurs are related to birds based on anatomical similarities. This observation is based on comparisons of dinosaur models constructed from fossil evidence, and modern birds that are alive today.
In 2007, scientists discovered protein sequence-based evidence supporting the hypothesis that dinosaurs are related to modern species of birds. This article was published in Science: "Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry."
In this paper, the scientists isolated protein fragments from a 68-million-year-old fossilized bone!
In this activity, we are going to use one of the protein sequences from this scientific paper, as well as protein sequences from other organisms, to investigate the relatedness of the extinct Tyrannosaurus rex with modern animal species.
We are going to construct our trees using a gene called alpha-2 type I collagen, which is a protein found in most connective tissues.
Question: DNA and protein sequences can both be used to construct a phylogenetic tree. How do you think DNA and protein might give different information? Hint: the genetic code is "degenerate."
Question: Let's take a look at these sequences. What do you notice about the T. rex protein sequence and the sequences from the other species?
Align protein sequences and compute a phylogenetic tree
First, we will align our sequences with muscle
We will copy and paste the protein sequences into the input box:
After we paste the sequences, we will click the "Submit" button
When the alignment job is running, you will see this message:
We are interested in two sections of the results page:
Let's scroll down the page and examine the multiple sequence alignment. What do you notice?
Now, let's navigate to the "Phylogenetic Tree" tab on our results page.
Question: What does the tree tell us about the relatedness of T. rex and the other species?
Use BLAST to search for sequences with similarity to the T. rex protein sequence
Click the button below to go to blastp
Copy and paste your sequence into the Query Sequence box on the BLAST page
Click the "BLAST" button at the bottom of the page
The top results are shown in descending order. The top hit is a "self hit" to the sequence we just BLASTed.
Question: Which species have sequences with significant similarity to the T. rex sequence? Does the BLAST result agree or disagree with our phylogenetic tree?
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