DICTIONARIES (CONT.)

CSE111Bio:ProgramDesignILecture24:Phylogenetictrees

RobertSloan(CS)&RachelPoretsky(Bio)UniversityofIllinois,Chicago

November21,2017

https://imgs.xkcd.com/comics/tree.png

TuesdayafterThanksgiving

• About5minutesofclasswillbespentonCSdepartmentClimatesurvey

• AdministeredinCS111,141,andCS251eachfallbyCSstudentaffairsstaff

• Easytodoonyourphone,butbringlaptopifyoupreferthat

DICTIONARIES(CONT.)

def translate():d = {"hello":"hola", "goodbye":"adios", "good":"bueno", "spam":"spam"}for word in d:

print(word, "is: ", d[word])d["more"] = "mas"

translate() A. hello is: holagoodbye is: adiosgood is: buenospam is: spam

B.good is: buenohello is: holagoodbye is: adiosspam is: spam

C. E. A or D or otherhello is: holagoodbye is: adiosgood is: buenospam is: spammore is: mas

D.spam is: spamgood is: buenogoodbye is: adioshello is: hola

def translate():d = {"hello":"hola", "goodbye":"adios", "good":"bueno", "spam":"spam"}for word in d:

print(word, "is: ", d[word])d["more"] = "mas"

translate()good is: buenohello is: holagoodbye is: adiosspam is: spam

Theorderisweird!

TryThis…

>>> score(“spam”, scrabble_dict)8

def score(myString, dict):

Youcanusewhileorforloopshere…

scrabble_dict = {"a":1, "b":3, "c":3, "d":2, …}

TryThis…

scrabble_dict = {"a":1, "b":3, "c":3, "d":2, …}

def score(my_string, dict):total = 0for letter in my_string:

total += scrabble_dict[letter]return total

Usefulmethod(fromZybook)

• d.get(key)isalternatesyntaxford[key]– Okay,fine,butwhere'stheadvantage?

• d[key-not-in-d]à KeyError• d.get(key,default)à d[key]ifkeyand defaultotherwise

– E.g.,d.get(key,"N/A")

Dictionary,ohhowdoIlovethee?

• ListsinPythonarewonderful,andamazing• Theonethingthatmightbebetterisdictionaries• All-purposeforkey-valuelinkages

– Ifyou'reGoogleandwanttoremembereverypagethathasthephrase"TreeofLife"onit?

• Dictionarywithstringkeys,andlistofstrings(URLS)values

– Doinganysortoftranslation,rangingfromEnglishtoSpanishtomRNAtoAminoacids?

– Etc.?

TREES

• AlllifeonEarthevolvedfromacommonancestor.

• Biologistsmaphoworganismsarerelatedbyconstructingphylogenetictrees.

Figure12.2

• Recentgeneticanalysisandotheradvancementshavefoundthatsomeearliertaxonomicclassificationsdonotreflectactualevolutionaryrelationships,andtherefore,changesandupdatesmustbemadeasnewdiscoveriestakeplace.

• Onedramaticandrecentexamplewasthebreakingapartofprokaryoticspecies,whichuntilthe1970swereallclassifiedasbacteria.

• TheirdivisionintoArchaea andBacteriacameaboutaftertherecognitionthattheirlargegeneticdifferenceswarrantedtheirseparationintotwoofthreefundamentalbranchesoflife.

=Whatreallymatters?

Treescanbedrawnindifferentways

Morerecentcommonancestor

Figure12.4

Aphylogenetictreeisrootedandshowshowdifferentorganisms,inthiscasethespeciesandsubspeciesoflivingapes,evolvedfromacommonancestor.

Branchpoint

Sistertaxa

Figure12.5

• Thisphylogenetictreeisrootedbyanorganismthatlackedavertebralcolumn.Ateachbranchpoint,organismswithdifferentcharactersareplacedindifferentgroups.

Figure12.6

Organismsthatsharesimilarphysicalfeaturesandgeneticsequencestendtobemorecloselyrelatedthanthosethatdonot.Featuresthatoverlapbothmorphologicallyandgeneticallyarereferredtoashomologousstructures;thesimilaritiesstemfromcommonevolutionarypaths.

Figure12.7

Someorganismsmaybeverycloselyrelated,eventhoughaminorgeneticchangecausedamajormorphologicaldifferencetomakethemlookquitedifferent.

Figure12.8

Unrelatedorganismsmaybedistantlyrelatedyetappearverymuchalike,usuallybecausecommonadaptationstosimilarenvironmentalconditionsevolvedinboth.

timeà

PhylogenyofSpecies:Atree-likerepresentationofevolutionaryrelationshipsamongspecies)

Commonlyusedinbasicevolutionaryresearch,conservation,andmedicine.

timeà

timeà

timeà

timeà

timeà

Isthefrogmorecloselyrelatedtothefishorthehuman?

a. Fishb. Humanc. Equallyrelatedtobothd. Thereisnotenoughinformationtodecide

timeà

Isthefrogmorecloselyrelatedtothefishorthehuman?

a. Fishb. Humanc. Equallyrelatedtobothd. Thereisnotenoughinformationtodecide

timeà

Which taxon on the tree below is most closely related to taxon D?

a. Ab. Bc. Cd. All of the above are

equally closelyrelated to D

Which taxon on the tree below is most closely related to taxon C?

a. Ab. Bc. Dd. B and D are

equally closely related to C

e. All of the above areequally closelyrelated to C

Which taxon on the tree below is most closely related to taxon A?

a. Bb. Cc. Dd. All of the above are

equally closely related to A

MostStudiedGeneSequences

• Rubisco (fromchloroplast,rbcL)• Ribosomesubunits(fromnucleus,18S&26S)• ATPsynthase(fromchloroplast,atpB)

Manyofthealgorithmsdevelopedforphylogenetics havebeenusedtodevelopsoftwareinotherfields.

MolecularsystematicsTheuseofDNAandRNAsequencestoinferevolutionaryrelationships

• Manymoremolecularcharactersavailableforanalysisthanmorphologicalones.

• Identityiseasiertodefine:ATCGvs.whetheraflowercolorispinkorwhite.

Forexample,twoplantsmayhavea“C”ataparticularlocationonagene

• Onepossibilityisthattheyhaveevolvedtogetherandarecloselyrelated

• Anotherpossibilityisthatonestartedatwiththe“C”atthatlocationanditdidn’tchange,whiletheotherplantwent“C->G->A->T->C”andlookslikeit’sthesameevolutionbecauseallyouseeisthestartandfinish“C”

ModernPhylogenetics

• DNAsequencedataarenowoverwhelminglythetoolofchoiceforgeneratingphylogenetichypotheses.

• Muchofthisdataisontheweb.

• NationalCenterforBiotechnologyInformationhttp://www.ncbi.nlm.nih.gov/

Figure12.9

• Lizards,rabbits,andhumansalldescendfromacommonancestorinwhichtheamnioticeggevolved.Thus,lizards,rabbits,andhumansallbelongtotheclade Amniota.Vertebrataisalargercladethatalsoincludesfishandlamprey.

Elephants (Loxodonta sp.)

MacGillivray’s warbler(Oporornis tolmieli)

Influenza A

Approximatemolecularclock:thenumberofDNAsubstitutionsinconstantovertime.

RelevancetoCS?Choosingtherightrelationships:

• Constructingaphylogenetictree,orcladogram,fromthecharacterdataisamonumentaltaskthatisusuallyleftuptoacomputer.

• Thecomputerdrawsatreesuchthatallofthecladessharethesamelistofderivedcharacters

http://evolution.genetics.washington.edu/phylip/newicktree.html

TheNewick Standardforrepresentingtreesincomputer-readableformmakesuseofthecorrespondencebetweentreesandnestedparentheses,noticedin1857bythefamousEnglishmathematicianArthurCayley.Ifwehavethisrootedtree:

theninthetreefileisrepresentedby:(B,(A,C,E),D)

((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700,seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,weasel:18.87953):2.09460):3.87382,dog:25.46154)

"HomosapiensisamemberofthegroupHomo,whichisamemberofthegroupHomininae”

Childtoparent

"Primatescontainstwogroups:Haplorrhini andStrepsirrhini”

Parenttochild

"HomosapiensisamemberofthegroupHomo,whichisamemberofthegroupHomininae”

Childtoparent

tax_dict = {'Homo sapiens' : 'Homo','Homo' : 'Homininae'

}

def get_ancestors(taxon):first_parent = tax_dict.get(taxon)second_parent = tax_dict.get(first_parent)third_parent = tax_dict.get(second_parent)return[first_parent, second_parent, third_parent]

def get_ancestors(taxon):result = [taxon]while taxon != 'Primates':

result.append(tax_dict.get(taxon))taxon = tax_dict.get(taxon)

return result

Noticehoweachtimeroundtheloopwesetthevalueofthetaxonvariabletobethenameoftheparenttaxon,whichthenbecomesthechildinthenextiterationofthewhileloop.


Parenttochild

tax_dict = {'Strepsirrhini' : 'Lorisidae','Strepsirrhini' : 'Lemuriformes','Strepsirrhini' : 'Lorisiformes'

}

Whyisthisnogood?


Parenttochild

new_tax_dict = { 'Primates': ['Haplorrhini', 'Strepsirrhini'],

}

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DICTIONARIES (CONT.)