Download genetics_phylogeny_exercise

Using the protein sequence for human beta globin do a BLASTP search in the UCSD Biology
WorkBench using the SwissProt database. Using CLUSTALW and other tools we learned in
this weeks tutorials, answer the following:
Based on the CLUSTALW alignment and DRAWTREE evolutionary trees generated from the
alignment of beta globin proteins from mountain gorilla, pigs, rabbits, dogs, badger, otter,
bats, pandas and chimpanzees, what conclusions can you draw about the evolution of beta
globin? Can you use this information to extrapolate about the evolutionary histories of
these animal lineages? EXPLAIN why or why not? (click here for organism ID information)
I was unable to find the required species from the available listings (GORBE, CANFA,
ROUAE did not appear anywhere in the list of returned options), therefore, I selected
the following:
Selected Sequence(s)
 Hemoglobin subunit beta-1/2 [Oryctolagus cuniculus (Rabbit)]
 Hemoglobin subunit beta [Ailuropoda melanoleuca (Giant panda)]
 Hemoglobin subunit beta [Meles meles (Eurasian badger)]
 Hemoglobin subunit beta [Lutra lutra (European river otter)]
 Hemoglobin subunit epsilon [Sus scrofa (Pig)]
 Hemoglobin subunit epsilon [Gorilla gorilla gorilla (Lowland gorilla)]
 Hemoglobin subunit epsilon [Pan troglodytes (Chimpanzee)]
 Hemoglobin subunit epsilon [Macaca mulatta (Rhesus macaque)]
 Hemoglobin subunit epsilon [Pongo pygmaeus (Bornean orangutan)]
Consensus key (see documentation for details)
* - single, fully conserved residue
: - conservation of strong groups
. - conservation of weak groups
- no consensus
CLUSTAL W (1.81) multiple sequence alignment
HBE_PANTR
HBE_GORGO
HBE_PONPY
HBE_MACMU
HBE_PIG
HBB_LUTLU
HBB_AILME
HBB_MELME
HBB_RABIT
MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPK
MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPK
MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPK
MVHFTAEEKAAVTSLWSKMNVEETGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPK
MVHFTAEEKSVITGLWGKVNVEETGGQAVGRLLVVYPWTQRFFDSFGNMSSPSAIMGNPK
-VHLTGEEKAAVTSLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSPDAVMGNPK
MVHLTGEEKAAVTGLWSKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSTPDAVMNNPK
-VHLTAEEKSAVTSLWGKVNVDEVGGEALGRLLVVYPWTQRYFDSFGDLSTPDAVMGNPK
MVHLSSEEKSAVTALWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNNPK
**::.***:.:*.**.*:**:*.**:*:************:*:***::*:..*::.***
HBE_PANTR
HBE_GORGO
HBE_PONPY
HBE_MACMU
HBE_PIG
HBB_LUTLU
HBB_AILME
VKAHGKKVLTSFGDAIKNMDNLKPAFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFG
VKAHGKKVLTSFGDAIKNMDNLKPAFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFG
VKAHGKKVLTSFGDAIKNMDNLKTTFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFG
VKAHGKKVLTSFGDAIKNMDNLKITFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFG
VKAHGKKVLTAFGDAVKNMDNLKGTFAKLSELHCDKLHVDPENFRLLGNMIVIILASHFG
VKAHGKKVLNSFSEGLKNLDNLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFG
VKAHGKKVLNSFSEGLKNLDNLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFG
HBB_MELME
HBB_RABIT
VKAHGKKVLNSFSEGLKNLDNLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFG
VKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFG
********* :*.:.:.::**** :*******************:****::* :*: ***
HBE_PANTR
HBE_GORGO
HBE_PONPY
HBE_MACMU
HBE_PIG
HBB_LUTLU
HBB_AILME
HBB_MELME
HBB_RABIT
KEFTPEVQAAWQKLVSAVAIALAHKYH
KEFTPEVQAAWQKLVSAVAIALAHKYH
KEFTPEVQAAWQKLVSAVAIALAHKYH
KEFTPEVQAAWQKLVSAVAIALAHKYH
GEFTPEVQAAWQKLVAGVATALAHKYH
KEFTPQVQAAYQKVVAGVANALAHKYH
KEFTPQVQAAYQKVVAGVANALAHKYH
KEFTPQVQAAYQKVVAGVANALAHKYH
KEFTPQVQAAYQKVVAGVANALAHKYH
****:****:**:*:.** *******
a. Paste your BOXSHADE output here:
b. Paste your unrooted tree here:
c. Paste your rooted tree here:
Given the above data, I’d propose that the evolutionary histories of these animal lineages
are quite similar, as far as the evolution of beta-globin is concerned. As indicated by the
BOXSHADE output, the alignment of the beta-globin amino acid sequence is very often fully
conserved across each species. Both the unrooted and rooted phylogenetic trees show
greater segmentation among the selected species. PANTR, GORGO, PONPY and MACMU are
all relatively close in their genetic makeup of beta-globin, whereas LUTLU, AILME, MELME
and RABIT share closeness with each other in a cluster separate from the primate group.
PIG represents a section of species equidistant between the ruminants and primates, to the
extent of evolutionary divergence of the beta-globin gene.
2. Go back and BLAST the myoglobin sequence as in the tutorial. Produce a rooted and
unrooted tree for vertebrates from a multiple alignment pick the same species as above.
I recognize that the same species have not been selected, however, as there were
different workbench labels when aligning the different proteins, I had to select what
was available.
Selected Sequence(s)
 Myoglobin [Ailuropoda melanoleuca (Giant panda)]
 Myoglobin [Meles meles (Eurasian badger)]
 Myoglobin [Oryctolagus cuniculus (Rabbit)]
 Myoglobin [Lutra lutra (European river otter)]
 Myoglobin [Sus scrofa (Pig)]
 Myoglobin [Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)]
 Myoglobin [Pongo pygmaeus (Bornean orangutan)]
 Myoglobin [Gorilla gorilla beringei (Mountain gorilla) (Highland gorilla)]
 Myoglobin [Pan troglodytes (Chimpanzee)]
Consensus key (see documentation for details)
* - single, fully conserved residue
: - conservation of strong groups
. - conservation of weak groups
- no consensus
CLUSTAL W (1.81) multiple sequence alignment
MYG_PANTR
MYG_GORBE
MYG_PONPY
MYG_MACFA
MYG_PIG
MYG_RABIT
MYG_MELME
MYG_AILME
MYG_LUTLU
MYG_PANTR
MYG_GORBE
MYG_PONPY
MYG_MACFA
MYG_PIG
MYG_RABIT
MYG_MELME
MYG_AILME
MYG_LUTLU
MYG_PANTR
MYG_GORBE
MYG_PONPY
MYG_MACFA
MYG_PIG
MYG_RABIT
MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE
MGLSDGEWQLVLNVWGKVEADISGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE
MGLSDGEWQLVLNVWGKVEADIPSHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE
MGLSDGEWQLVLNVWGKVEADIPSHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE
MGLSDGEWQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE
MGLSDAEWQLVLNVWGKVEADLAGHGQEVLIRLFHTHPETLEKFDKFKHLKSEDEMKASE
MGLSDGEWQLVLNVWGKVEADLAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKGSE
-GLSDGEWQLVLNVWGKVEADLAGHGQEVLIRLFKGHPETLEKFDKFKHLKSE---KGSE
MGLSDGEWQLVLNVWGKVEADLAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKGSE
****.***************:..**********: *****************
*.**
DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLHSKH
DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH
DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISESIIQVLQSKH
DLKKHGVTVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLELISESIIQVLQSKH
DLKKHGNTVLTALGGILKKKGHHEAELTPLAQSHATKHKIPVKYLEFISEAIIQVLQSKH
DLKKHGNTVLTALGAILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISEAIIHVLHSKH
DLKKHGNTVLTALGGILKKKGHQEAELKPLAQSHATKHKIPVKYLEFISDAIAQVLQSKH
DLKKHGNTVETALEGILKKK---------------------------------------DLKKHGNTVLTALGGILKKKGKHEAELKPLAQSHATKHKIPIKYLEFISEAIIQVLQSKH
****** ** *** .*****
PGDFGADAQGAMNKALELFRKDMASNYKELGFQG
PGDFGADAQGAMNKALELFRKDMASNYKELGFQG
PGDFGADAQGAMNKALELFRKDMASNYKELGFQG
PGDFGADAQGAMNKALELFRNDMAAKYKELGFQG
PGDFGADAQGAMSKALELFRNDMAAKYKELGFQG
PGDFGADAQAAMSKALELFRNDIAAQYKELGFQG
MYG_MELME
MYG_AILME
MYG_LUTLU
PGNFAAEAQGAMKKALELFRNDIAAKYKELGFQG
--------------ALELFKNDIAAKTKELGFLG
PGDFGADAQGAMKRALELFRNDIAAKYKELGFQG
*****::*:*:: ***** *
a. Paste your BOXSHADE output here:
b. Paste your unrooted tree here:
c. Paste your rooted tree here:
3. Is the beta globin tree the same as the myoglobin tree? EXPLAIN what this means with
regard to inferring evolutionary relationships among these species.
Although the trees are similar, they are not the same. These trees each represent the
phylogenesis of the different species, and as such, depict the ancestry of the species in
regards to the development of their myologin and beta-globin genes. In other words, we
cannot tell the proximity of relationship from the trees, but we can infer, for example, that
MELME and AILME are more closely related in their genetics than RABIT and LUTLU.