Big Idea 1

Phylogeny Project

 

>human
MASEFKKKLFWRAVVAEFLATTLFVFISIGSALGFKYPVGNNQTAVQDNVKVSLAFGLSI
ATLAQSVGHISGAHLNPAVTLGLLLSCQISIFRALMYIIAQCVGAIVATAILSGITSSLT
GNSLGRNDLADGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSAPLAIGLSVALGH
LLAIDYTGCGINPARSFGSAVITHNFSNHWIFWVGPFIGGALAVLIYDFILAPRSSDLTD
RVKVWTSGQVEEYDLDADDINSRVEMKPK

 

>rat
MASEIKKKLFWRAVVAEFLAMTLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSI
ATLAQSVGHISGAHLNPAVTLGLLLSCQISILRAVMYIIAQCVGAIVASAILSGITSSLL
ENSLGRNDLARGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSAPLAIGLSVALGH
LLAIDYTGCGINPARSFGSAVLTRNFSNHWIFWVGPFIGSALAVLIYDFILAPRSSDFTD
RMKVWTSGQVEEYDLDADDINSRVEMKPK

 

>bovine
MASEFKKKLFWRAVVAEFLAMILFIFISIGSALGFHYPIKSNQTTGAVQDNVKVSLAFGL
SIATLAQSVGHISGAHLNPAVTLGLLLSCQISVLRAIMYIIAQCVGAIVATAILSGITSS
LPDNSLGLNALAPGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSGPLAIGFSVAL
GHLLAIDYTGCGINPARSFGSSVITHNFQDHWIFWVGPFIGAALAVLIYDFILAPRSSDL
TDRVKVWTSGQVEEYDLDADDINSRVEMKPK

 

>doge
MASEFKKKLFWRAVVAEFLAMILFVFISIGSALGFNYPVRNNQTAGAAQDNVKVSLAFGL
SIATLAQSVGHISGAHLNPAVTLGLLLSCQISILRAVMYIIAQCVGAIVATAILSGITSS
LPDNSLGRNELAPGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSGPLAIGLSVAL
GHLLAIDYTGCGINPARSFGSSVITHNFKDHWIFWVGPFIGGALAVLIYDFILAPRSSDL
TDRVKVWTSGQVEEYELDGDDINSRVEMKPK

 

>mouse ear cress
MAGVAFGSFDDSFSLASLRAYLAEFISTLLFVFAGVGSAIAYAKLTSDAALDTPGLVAIA
VCHGFALFVAVAIGANISGGHVNPAVTFGLAVGGQITVITGVFYWIAQLLGSTAACFLLK
YVTGGLAVPTHSVAAGLGSIEGVVMEIIITFALVYTVYATAADPKKGSLGTIAPLAIGLI
VGANILAAGPFSGGSMNPARSFGPAVAAGDFSGHWVYWVGPLIGGGLAGLIYGNVFMGSS
EHVPLASADF

 

>mouse
MASEIKKKLFWRAVVAEFLAMTLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSI
ATLAQSVGHISGAHLNPAVTLGLLLSCQISILRAVMYIIAQCVGAIVATAILSGITSSLV
DNSLGRNDLAHGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSAPLAIGLSVALGH
LLAIDYTGCGINPARSFGSAVLTRNFSNHWIFWVGPFIGGALAVLIYDFILAPRSSDFTD
RMKVWTSGQVEEYDLDADDINSRVEMKPK

 

>fruit fly
MGAREDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIEVDGKTI
KAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIM
LVGNKSDLRHLRSVPTDEAKLFAERNGLSFIETSALDSTNVETAFQNILTEIYRIVSQKQ
IRDPPEGDVIRPSNVEPIDVKPTVTADVRKQCCQ

 

>slime mold
MSLKRSDDYQDLEEGIAMEDGGNIKDEEEKPLDPIEEQNKKRWVLIRAVLGELLCTFLFV
YVLCATSANFIRLGSPPNPVVGGLSTGFAAVALIYSFADVSGAHFNPAVTFATCVTRKTS
ITKGLMYVGAQLVGSVLASLILLATFPGNFPGDKNAASAVAIAPSTDANIGNAFLTELVL
TFILVYVIFAVAFDTVDNSVKTKVVGKSSSNNLTIYTTSGQTKAGFAPIAIGFTLGFLCF
LGGSVSGGAFNPARVFGTALVGNNWTRHWMYWIADFLGAGLAGFAQKFFSSTHK

 

>baker’s yeast
MSSNDSNDTDKQHTRLDPTGVDDAYIPPEQPETKHHRFKISRDTLRDHFIAAVGEFCGTF
MFLWCAYVICNVANHDVALVAAPDGSHPGQLIMIAIGFGFSVMFSIWCFAGVSGGALNPA
MSLSLCLARAVSPTRCVVMWVSQIVAGMAAGGAASAMTPGEVLFANSLGLGCSRTRGLFL
EMFGTAILCLTVLMTAVEKRETNFMAALPIGISLFIAHVALTAYTGTGVNPARSLGAAVA
ARYFPHYHWIYWIGTLLGSILAWSVWQLLQILDYTTYVTAEKAASTKEKAQKKGETSSSS
AVAEV

 

>sheep
MASEFKKKLFWRAVVAEFLAMILFIFISIGSALGFHYPIKSNQTTGAVQDNVKVSLAFGL
SIATLAQSVGHISGAHLNPAVTLGLLLSCQISILRAIMYIIAQCVGAIVATVILSGITSS
LPDNSLGLNALAPGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRRDLGDSGPLAIGFSVA
LGHLLAIDYTGCGINPARSFGSSVITHNFQDHWIFWVGPFIGAALAVLIYDFILAPRSSD
LTDRVKVWTSGQVEEYDLDADDINSRVEMKPK

 

>strain k12
MFRKLAAECFGTFWLVFGGCGSAVLAAGFPELGIGFAGVALAFGLTVLTMAFAVGHISGG
HFNPAVTIGLWAGGRFPAKEVVGYVIAQVVGGIVAAALLYLIASGKTGFDAAASGFASNG
YGEHSPGGYSMLSALVVELVLSAGFLLVIHGATDKFAPAGFAPIAIGLALTLIHLISIPV
TNTSVNPARSTAVAIFQGGWALEQLWFFWVVPIVGGIIGGLIYRTLLEKRD

 

>pig
MASEFKKKIFWRAVVAEFLAMTLFIFISIGSALGFQYPVRNNQTSGAAQDNVKVSLAFGL
SIATLAQSVGHISGAHLNPAVTLGLLLSCQISVLRAVMYIIAQCVGAIVATAILSGITSS
LPGNSLGLNSLAPGVDSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSAPLAIGFSVAL
GHLLAIDYTGCGINPARSFGSAVITHNFQDHWVFWVGPFIGGALAVLIYDFILAPRSSDL
TDRVKVWTSGQVEEYDLDGDDINSRVEMKPK

 

>maize
MEGKEEDVRLGANKFSERHAIGTAAQGTDDKDYKEPPPAPLFEPGELKSWSFYRPGIAEF
VATFLFLYISILTVMGVSKSTSKCATVGIQGIAWSFGGMILALVYCTAGISGHINPAVTF
GLFLARKLSLTRAVFYIIMQCLGAICGRGVVKGFQQGLYMGNGGRRNVVAPGYTKGDGLG
AEIVGTFILVYTVFSATDAKRRARDSHVPILAPLPIGFAVFLVHLATMGITGTGINPARS
LGAAVIYNQHHAWADHWIFWVGPFIGAALAAIYHQVIIRAIPFKSRS

 

>guinea pig
MWELRSASFWRAIFAEFFATLFYVFFGLGASLRWAPGPLHVLQVALAFGLALAXLVQTVG
HISGAHVNPAVTFXFLVGSQMSLLRAFCYMAAQLLGAVAGAAVLYSVTPPAVRGNLALNT
LHAGVSVXQATTVEIFLTLQFVLCIFATYDERRNGRLGSVALAVGFSLTLGHLFGMYYTG
AGMNPARSFAPAILTRNFTNHWVYWVGPIIGGGLGSLLYDFLLFPRLKSVSERLSILKGT
RPSDNNGQPEGTGEPVELKTQAL

 

>rice
MPIRNIAVGSHQEVYHPGALKAALAEFISTLIFVFAGQGSGMAFSKLTGGGATTPAGLIA
AAVAHAFALFVAVSVGANISGGHVNPAVTFGAFVGGNITLFRGLLYWIAQLLGSTVACFL
LRFSTGGLATGTFGLTGVSVWEALVLEIVMTFGLVYTVYATAVDPKKGSLGTIAPIAIGF
IVGANILVGGAFDGASMNPAVSFGPALVSWSWESQWVYWVGPLIGGGLAGVIYEVLFISH
THEQLPTTDY

 

>chicken
MGNRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTI
KAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIM
LVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQKQ
MSDRRENDMSPSNNVVPIHVPPTTENKPKMQCCQNI

screen-shot-2016-10-05-at-7-27-40-pm
screen-shot-2016-10-05-at-7-41-29-pmscreen-shot-2016-10-05-at-7-41-47-pmscreen-shot-2016-10-05-at-7-41-59-pmscreen-shot-2016-10-05-at-7-42-12-pmscreen-shot-2016-10-05-at-7-42-24-pm

The concept that all life on Earth is related is a central tenet of Darwin’s theory of evolution, so I knew right off the bat that all of the organisms I would be experimenting with, would be related. Conserved core processes are processes that provide evidence that all organisms are linked by lines of descent from common ancestry. I can conclude that there are conserved core processes present, even though there are organism so seemingly different; like homo sapiens and baker’s yeast. Since I know the organisms I have selected share a common ancestor, I know that different species have arised during speciation. Before entering my FASTA sequences into tcoffee or phylogeny.fr, I assumed that the genes were very widely distributed. I also assumed that certain organisms would not be closely related at all, and was generally assuming that mouse and rat would be closely related, or maybe pig and guinea pig, but was very surprised to see that fruit flies and chicken are closely related because of how different their phenotypes are.

My alignment in tcoffee is very confusing in general, and I am having a hard time figuring out exactly what it means by “good” vs. “bad”. Is that the equivalent of weak vs. poor?  My phylogeny tree and alignment seem to correspond with each other hand in hand. I can see when reviewing my alignment, it appears that the same organisms are closely related as it does in my tree. A challenge presented that greatly complicates phylogenetic inference is the occurrence of convergent and parallel evolution, which lead to lineages becoming more similar to each other over time. When organisms become more similar over time, this process is known as homoplasy. This becomes critical issue for phylogenetic analysis because only traits that are homologous and in which the observed similarities are not due to convergence or parallel evolution should be compared and contrasted.

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