Milena Kovářová 28 07 2011 Informatics view of determining the relationship between organisms Imagine the situation you have find some new so far unknown organism And you want to ID: 751935
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Slide1
Lenka
KovářováSupervisor: Milena Kovářová
28. 07. 2011
Informatics view of determining
the relationship between
organismsSlide2
Imagine the situation you have find some new so far unknown organism
And
you
want to know some relative species of organismsWhtat to do know
?
Ask
the unknown organismIt would probably not answerFind some similar signs to known organismsThat is not a proof of their relationshipFind genomic similaritySlide3
How
to
compare genome
Compare whole DNA codeTheat is a big amount of dataCompare selected chromosome
Relative
s
pecies can have the same gene on different locations of different chromosomesCompare one special geneYou don’t know where to find selected gene in gemone of far unknown organismAlmost all eucatyotic organisms has mitochondrial DNASlide4
Mitochondrion
Semi–autonomic
organele
Found in most eukaryotic cellsDescribed as cellular power plantsHas its own independent
genome
Believed to be originally derived from endosymbiotic prokaryotesSlide5
Mitochondrial DNA
Mostly circular DNA moleculeSlide6
Mitochondrial inheritance
Mitochondria
are normally inherited exclusively from the motherMitochondrial DNA is not highly conserved and has a rapid mutation rateIt is useful for studying the evolutionary relationships of organisms
M
odel
of human migration based on Mitochondrial DNASlide7
Project
Try
to
determnine the relationship between organisms based on mitochondrail DNADownload as many mitochondial
DNA
of
different organisms as possibleMake a program of suiatable algorithm to determine the similarity of DNA codeAnalyse the resultsSlide8
Eukaryota
Viridi
plantaeStrepto phytaStrepto phytinaEmbryo phyta
Tracheo phytaEuphyllo phytaSpermato phyta
Magnolio
phytaEudicotyl edonsrosidsmalvidsBrassicales
Brassi caceae
Camelineae
Arabi dopsis
Arabidopsis
thaliana
Bryophyta
Bryophytina
Bryopsida
Funariidae
Funariales
Funariaceae
Physcomitrella
Physcomitrella patens
Physcomitrella patens
Opistho
konta
Fungi
Dikarya
Ascomy
cota
saccharomycetaPezizomy cotinaleotiomycetaEurotiomy cetesEurotiomy cetidaeEurotialesTrichocomaceaeAspergillusAspergillus nigerAspergillus nigerSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomy cetaceaeEremothe ciumEremothecium gossypiiAshbya gossypiiSaccharomycesSaccharomyces cerevisiaeSaccharomyce cerevisiaeMetazoaBilateriaProto stomiaPanarthro podaArthropodaMandibulataPancru staceaHexapodaInsectaDicondyliaPterygotaNeopteraParaneo pteraHemi pteraSterno rrhynchaAphidi formesAphido morphaAphidoideaAphididaeAphi dinaeMacro siphiniAcyrtho siphonAcyrthosiphon pisumEndoptery gotaHymenopteraApocritaAculeataApoideaApidaeApinaeApiniApisApis melliferaColeopteraPolyphagaCucujiformiaTenebrionoideaTenebrionidaeTriboliumTribolium castaneumDeute rostomiaEchino dermataEleuthero zoaEchinozoaEchinoideaEuechinoideaEchinaceaEchinoidaStrongylo centrotidaeStrongylo centrotusStrongylocentrotus purpuratusHemi chordataEntero pneustaHarrimanii daeSacco glossusSaccoglossus kowalevskiiChordataTunicataAscidiaceaCionidaeCionaCiona intestinalisCraniataVertebrataEuteleostomiActinopterygiiActinopteriNeopterygiiTeleosteiElopoc ephalaClupeo cephalaOto cephalaOstario physiOtophysiCyprini physiCyprini formesCyprinoi deaCyprini daeDanioDanio rerioSarcopterygiiTetrapodaAmphibiaBatrachiaAnuraMesoba trachiaPipoi deaPipidaeXenopodinaeXenopusSiluranaXenopus tropicalisAmniotaSauropsidaSauriaLepidosauriaSqua mataIguaniaIguani daePoly chrotinaeAnolisAnolis carolinensisArchosauriaDinosauriaSaurischiaThero podaAvesNeognathaePasseri formesPasseroideaEstril didaeTaenio pygiaTaeniopygia guttataGalli formesPhasianidaePhasianinaeGallusGallus gallusMeleagri dinaeMeleagrisMeleagris gallopavoMammaliaPrototheriaMonotre mataOrnithorhynchidaeOrnithorhynchusOrnithorhynchus anatinusTheriaMetatheriaDidelphimorphiaDidelphidaeDidelphinaeMonodelphisMonodelphis domesticaEutheriaLaurasiatheriaCarnivoraCaniformiaUrsidaeAiluropodaAiluropoda melanoleucaCanidaeCanisCanis lupusCanis familiarisCetartiodactylaRuminantiaPecoraBovidaeBovinaeBosBos taurusSuinaSuidaeSusSus scrofaPerissodactylaEquidaeEquusEquusEquus caballusEuarchontogliresGliresLagomorphaLeporidaeOryctolagusOryctolagus cuniculusRodentiaSciurognathiMuroideaMuridaeMurinaeMusMusMus musculusRattusRattus norvegicusPrimatesHaplorrhiniSimiiformesCatarrhiniCercopithecoideaCercopithecidaeCercopithecinaeMacacaMacaca mulattaHominoideaHominidaePonginaePongoPongo abeliiHomininaePanPan troglodytesHomoHomo sapiens
TaxonomySlide9
Vertebrata
Euteleostomi
ActinopterygiiActinopteriNeopterygiiTeleostei
Elopoc ephalaClupeo cephalaOto cephala
Ostario
physiOtophysiCyprini physiCyprini formesCyprinoi
dea
Cyprini dae
Danio
Danio rerio
Sarcopterygii
Tetrapoda
Amphibia
Batrachia
Anura
Mesoba
trachia
Pipoi
dea
Pipidae
Xenopodinae
Xenopus
Silurana
Xenopus
tropicalis
AmniotaSauropsidaSauriaLepidosauriaSqua mataIguaniaIguani daePoly chrotinaeAnolisAnolis carolinensisArchosauriaDinosauriaSaurischiaThero podaAvesNeognathaePasseri formesPasseroideaEstril didaeTaenio pygiaTaeniopygia guttataGalli formesPhasianidaePhasianinaeGallusGallus gallusMeleagri dinaeMeleagrisMeleagris gallopavoMammaliaPrototheriaMonotre mataOrnithorhynchidaeOrnithorhynchusOrnithorhynchus anatinusTheriaMetatheriaDidelphimorphiaDidelphidaeDidelphinaeMonodelphisMonodelphis domesticaEutheriaLaurasiatheriaCarnivoraCaniformiaUrsidaeAiluropodaAiluropoda melanoleucaCanidaeCanisCanis lupusCanis familiarisCetartiodactylaRuminantiaPecoraBovidaeBovinaeBosBos taurusSuinaSuidaeSusSus scrofaPerissodactylaEquidaeEquusEquusEquus caballusEuarchontogliresGliresLagomorphaLeporidaeOryctolagusOryctolagus cuniculusRodentiaSciurognathiMuroideaMuridaeMurinaeMusMusMus musculusRattusRattus norvegicusPrimatesHaplorrhiniSimiiformesCatarrhiniCercopithecoideaCercopithecidaeCercopithecinaeMacacaMacaca mulattaHominoideaHominidaePonginaePongoPongo abeliiHomininaePanPan troglodytesHomoHomo sapiensVertebrataTaxonomySlide10
Organisms
Streptophyta
Arabidopsis thaliana
Physcomitrella patensSlide11
Organisms
Fungi
Aspergillus
nigerAshbya gossypiiSaccharomyces cerevisiaeSlide12
Organisms
Insecta
Apis
melliferaAcyrthosiphon pisumTribolium castaneumSlide13
Organisms
Deuterostomia
Ciona
intestinalisSaccoglossus kowalevskiiStrongylocentrotus purpuratusSlide14
Organisms
Vertebrata
Anolis
carolinensisXenopus (Silurana) tropicalisDanio rerioSlide15
Organisms
Aves
Gallus
gallusMeleagris gallopavoTaeniopygia guttataSlide16
Organisms
Mammalia
Ornithorhynchus
anatinusMonodelphis domesticaSlide17
Organisms
Carnivora
Ailuropoda melanoleucaCanis familiarisSlide18
Organisms
Cetartiodactyla
Sus scrofaBos taurus PerissodactylaEquus
caballusSlide19
Glires
Oryctolagus
cuniculusMus musculusRattus norvegicus
OrganismsSlide20
Organisms
Primates
Macaca
mulattaPongo abeliiPan troglodytesHomo sapiensSlide21
Metodology
Get
the Fasta format of mitochondrial DNACompare the similarity
of
genomsFind relative organismsSlide22
Metodology
Compress
one DNA code and compress two DNA codes togetherCompare the
lenght
of compressed filesCompute the coefficients of similarity Where Compress(x) is the compression algorithm used on file x |x| is the length of file x and DNA1+DNA2 is the concatenation of DNA1 and DNA2 in this order
Coefficient ( DNA1,
DNA 2)= 1 -
|Compress( DNA1 )
|
– (
|
Compress
( DNA2
+
DNA1
)
|
-
|
Compress
( DNA2 )
|
)
|
Compress
( DNA1
+
DNA2 )|Slide23
Compress
algoritm
Deflate streamCombination of LZ77 algorithm and Huffman codingCompression is achieved through two stepsThe matching and replacement of duplicate strings with pointersReplacing symbols with new, weighted symbols based on frequency of useSlide24
Compress algorithm
Deflate
streamLossless data compression algorithm Combination of LZ77 algorithm and Huffman codingSeries of blocks, each block preceded by a 3-bit header1-bit: Last block in stream marker1: this is the last-block in the stream0: there are more blocks to process after this one2-bits: Encoding method used for this block type:00: a raw section follows, between 0 and 65,535 bytes in length
01: a
static Huffman
compressed block, using a pre-agreed Huffman tree10: a compressed block complete with the Huffman table supplied11: reserved, don't useSlide25
Algorithm LZ77
Duplicate string elimination
Within
compressed blocksIf a duplicate series of bytes is spotted (a repeated string)then a back-reference is insertedlinking to the previous location of that identical string insteadAn encoded match to an earlier string consists of a length (3–258 bytes) and a distance (1–32,768 bytes)Relative back-references can be made across any number of blocksSlide26
Huffman coding
Replacing
Commonly used symbols with shorter representations
Less commonly used symbols with longer representationsUnprefixed tree of non-overlapping intervalsLength of each sequence is inversely proportional to the probability of that symbol needing to be encodedA tree is created which contains space for 288 symbols0–255: represent the literal bytes/symbols 0–255.256: end of block257–285: combined with extra-bits, match length of 3–258 bytes286, 287: not usedSlide27
Huffman coding
A match length code will be followed by a distance code
Based on the distance code read, further "extra" bits may be read in order to produce the final distance.
The distance tree contains space for 32 symbols0–3: distances 1–44–5: distances 5–8, 1 extra bit6–7: distances 9–16, 2 extra bits8–9: distances 17–32, 3 extra bits...26–27: distances 8,193–16,384, 12 extra bits28–29: distances 16,385–32,768, 13 extra bits30–31: not usedSlide28
Number
of basis of mitochondrial DNA genomeStreptophyta Metazoa
Mammalia
366924
Arabidopsis
thaliana16969Acyrthosiphon pisum
17019
Ornithorhynchus anatinus
105338
Physcomitrella
patens
16343
Apis mellifera
17079
Monodelphis domestica
15881
Tribolium
castaneum
16805
Ailuropoda melanoleuca
Fungi
15650
Strongylocentrotus
purpuratus
16727
Canis familiaris31102Aspergillus niger 17037Saccoglossus kowalevskii16338Bos taurus23564Ashbya gossypii14790Ciona intestinalis16613Sus scrofa85779Saccharomyces cerevisiae16596Danio rerio16660Equus caballus17610Xenopus (Silurana) tropicalis17019Oryctolagus cuniculus17220Anolis carolinensis16299Mus musculus16853Taeniopygia guttata16313Rattus norvegicus16775Gallus gallus16564Macaca mulatta16719Meleagris gallopavo16499Pongo abelii16554Pan troglodytes16568Homo sapiensSlide29
Results
Arabidopsis
thalianaPhyscomitrella patensAspergillus niger
Ashbya gossypiiSaccharomyces cerevisiaeAcyrthosiphon pisumApis mellifera
Tribolium
castaneumStrongylocentrotus purpuratusSaccoglossus kowalevskiiCiona intestinalisDanio rerioXenopus
(Silurana) tropicalis
Anolis carolinensisTaeniopygia
guttataGallus
gallus
Meleagris
gallopavo
Ornithorhynchus
anatinus
Monodelphis
domestica
Ailuropoda
melanoleuca
Canis
familiaris
Bos
taurus
Sus
scrofaEquus caballusOryctolagus cuniculusMus musculusRattus norvegicusMacaca mulattaPongo abeliiPan troglodytesHomo sapiensArabidopsis th.0,00180,00260,0011-0,0008-0,00620,0001-0,00020,00150,00230,00200,00130,00230,00200,00210,00180,00170,00170,00200,00160,00200,00200,00190,00190,00190,00180,00190,00180,00180,00190,00190,0019Physcomitrella pat.0,00270,00570,0049-0,0011-0,01280,0011-0,00030,00550,00870,00730,00480,00800,00710,00680,00710,00680,00680,00750,00630,00750,00750,00690,00670,00700,00670,00680,00690,00710,00700,00700,0068Aspergillus niger 0,00170,00330,43300,0019-0,00050,00160,00310,00830,00840,00800,00760,00690,00710,00830,00680,00640,00760,00800,00800,00650,00630,00650,00540,00570,00470,00820,00660,00720,00680,00730,0071Ashbya gossypii0,0008-0,00200,00470,62450,00380,00500,00420,00150,00150,00230,0057-0,0001-0,00060,00130,00080,00070,0001-0,00070,00290,0013-0,0009-0,00230,0002-0,0002-0,00020,00130,0021-0,00030,0017-0,0006-0,0001Saccharomyces c.0,0007-0,0140-0,00120,00250,00440,00150,0012-0,0006-0,0040-0,0027-0,0002-0,0042-0,0039-0,0019-0,0038-0,0020-0,0037-0,0035-0,0031-0,0030-0,0039-0,0049-0,0033-0,0037-0,0038-0,0031-0,0030-0,0037-0,0024-0,0033-0,0036Acyrthosiphon pi.0,0010-0,00040,00660,00590,00200,71800,01490,01070,00350,00480,01070,00260,00330,00560,00320,00360,00420,00470,00680,00400,00270,00240,00390,00360,00430,00460,00380,00280,00360,00250,0034Apis mellifera0,0007-0,00160,00310,00530,00110,01000,73380,0060-0,00030,00140,00850,0014-0,00070,00330,00030,00170,0003-0,00060,00240,00150,0002-0,0023-0,0004-0,0003-0,00140,0025-0,00090,00110,0011-0,0004-0,0002Tribolium castan.0,00180,00500,01050,00220,00030,00870,00590,73370,01570,01430,01390,01550,01600,01370,01470,01300,01290,01350,01380,01520,01420,01410,01480,01370,01510,01600,01380,01450,01500,01460,0147Strongylocentrots p.0,00230,00720,0075-0,0008-0,0034-0,0001-0,00100,01050,70160,02120,01250,01990,01740,01630,01740,01750,01670,01770,01750,02030,01860,01760,01690,01930,01720,01820,01890,01790,01820,01790,0188Saccoglossus kow.0,00200,00610,0071-0,0002-0,00170,00290,00330,00770,01920,66220,00960,01670,01490,01680,01630,01390,01370,01550,01330,01450,01640,01430,01530,01490,01470,01510,01480,01370,01360,01450,0157Ciona intestinalis0,00130,00290,00900,00550,00150,00420,00480,01130,00790,00840,78960,00860,00990,00820,00620,00800,00880,00700,00820,00810,00650,00510,00670,00700,00680,00990,00740,00680,00700,00670,0064Danio rerio0,00210,00630,0055-0,0027-0,00430,0002-0,00300,00910,01890,01720,00880,64890,01640,01630,01740,01550,01670,01630,01390,01610,01670,01600,01610,01680,01400,01490,01670,01550,01750,01830,0154Xenopus tropicalis0,00240,00750,00960,0018-0,00230,00370,00270,01250,02310,02070,01180,02320,66510,02100,02130,02250,02080,02040,01960,02150,02080,02270,02210,02040,01960,02080,01980,02070,02080,02000,0222Anolis carolinensis0,00220,00650,0091-0,0007-0,00180,00370,00320,01130,01980,01690,01230,01780,01910,64770,01810,01760,01980,01700,01570,01980,01700,01820,01830,01990,01870,01940,01890,01740,01810,01810,0179Taeniopygia guttata0,00250,00680,0093-0,0006-0,00200,00210,00180,01380,02170,02040,01200,02190,02200,02020,67300,02850,02670,02190,02010,02210,01990,02160,02090,02010,01740,02020,01980,01930,01970,02080,0201Gallus gallus0,00220,00630,00850,0014-0,00210,00080,00050,00950,02010,01670,01220,01870,01720,01670,02180,67750,04170,01810,01510,01910,01710,01760,01700,01830,01680,01740,01730,01520,01600,01710,0165Meleagris gallopavo 0,00200,00660,00810,0006-0,00240,0013-0,00040,01050,01870,01930,01110,01820,01730,01880,02050,04750,65390,01830,01690,01890,01720,02000,01820,01830,01710,01840,01840,01850,01760,01730,0168Ornithorhynchus a.0,00210,00590,00750,0003-0,00240,00050,00180,00920,02150,01910,01170,02090,01920,01800,01890,01780,01720,65340,02140,02320,02210,02330,02350,02160,01960,02300,02270,01990,01910,02200,0211Monodelphis dom.0,00230,00700,01060,0030-0,00140,00570,00250,01210,02080,02140,01290,02030,01900,01790,02040,02020,02140,02310,66000,02390,02300,02410,02260,02300,02270,02620,02530,02020,02260,02230,0227Ailuropoda melanol.0,00200,00640,00720,0001-0,00360,0023-0,00030,01180,01990,01890,01030,02050,01680,01950,01980,01820,01700,01850,02080,61280,02750,02670,02200,02110,02300,02090,02530,02060,02260,02260,0196Canis familiaris0,00230,00630,00880,0004-0,00290,00020,00170,01040,02140,01980,01170,02140,01870,01910,02020,01870,01970,02390,02050,02740,68510,02880,02670,02670,02350,02820,02680,02280,02330,02520,0249Bos taurus0,00210,00630,00780,0005-0,0028-0,00010,00160,01060,02180,01830,01190,02130,01850,01910,01760,01930,01800,02090,01940,02790,02740,70890,02930,02850,02600,02550,02430,02170,02210,02410,0239Sus scrofa0,00210,00640,00900,0005-0,00260,00090,00160,01200,01820,01670,01190,01960,01820,01860,01590,01780,01720,02000,02020,02470,02440,03110,64580,02740,02750,02200,02600,02000,02220,02240,0200Equus caballus0,00230,00740,0084-0,0007-0,00230,00180,00370,01390,02260,01950,01330,02430,02010,01950,01910,01980,01870,02440,02180,02810,02900,03160,03070,75790,02560,02700,02740,02580,02370,02550,0270Oryctolagus cunic.0,00210,00680,00920,0012-0,00190,00350,00060,00960,02230,01890,01250,02210,01970,01880,01810,01770,01950,02310,02320,02690,02380,02710,02880,02530,68380,02800,02740,02590,02220,02280,0249Mus musculus0,0022
0,0067
0,0106
0,0025
-0,0006
0,0019
0,0041
0,0133
0,0206
0,0183
0,0140
0,0235
0,0183
0,0199
0,0184
0,0204
0,0187
0,0227
0,0231
0,0244
0,0227
0,0275
0,0270
0,0212
0,0240
0,7057
0,0439
0,0241
0,0201
0,0220
0,0233
Rattus
norvegicus
0,0023
0,0063
0,0088
0,0021
-0,0019
0,0023
0,0015
0,0114
0,0211
0,0193
0,0128
0,0198
0,0175
0,0183
0,0201
0,0203
0,0190
0,0216
0,0233
0,0258
0,0242
0,0304
0,0294
0,0242
0,0263
0,0456
0,7398
0,0257
0,0243
0,0262
0,0253
Macaca
mulatta
0,0023
0,0064
0,0092
0,0009
-0,0018
0,0033
0,0021
0,01270,02110,02000,01190,02200,01790,02040,01650,01860,01860,02020,02020,02490,02140,02260,02310,02230,02260,02350,02180,74920,02710,02710,0279Pongo abelii0,00240,00690,00980,0009-0,00130,00410,00580,01260,02140,02150,01330,02290,01950,02160,02000,02130,02060,02170,01990,02470,02120,02360,02590,02310,02330,02340,02640,03170,65080,03980,0416Pan troglodytes0,00230,00670,00840,0007-0,00210,00130,00300,01300,02140,02090,01230,02120,01900,01890,02030,01890,01830,02300,02020,02460,02220,02720,02440,02290,02310,02400,02760,02800,04020,75860,0784Homo sapiens0,00210,00650,0084-0,0005-0,00300,00140,00100,01000,02140,01850,01020,02040,01860,01840,01810,01700,01640,01940,01880,02390,02210,02330,02190,02080,02410,02070,02380,02660,03550,07410,7223
Coefficients of similarity
-
0,014 -0,007
-
0,007
-0,003
-
0,003
0,000
0,000 0,003
0,003
0,006
0,006
0,011
0,011
0,016
0,016
0,019
0,019
0,022
0,022
0,025
0,025
0,027
0,027
0,030
0,030
0,040
0,070
0,080Slide30
Results
Arabidopsis
thalianaPhyscomitrella patensAspergillus niger
Ashbya gossypiiSaccharomyces cerevisiaeAcyrthosiphon pisumApis mellifera
Tribolium
castaneumStrongylocentrotus purpuratusSaccoglossus kowalevskiiCiona intestinalisDanio rerioXenopus
(Silurana) tropicalis
Anolis carolinensisTaeniopygia
guttataGallus
gallus
Meleagris
gallopavo
Ornithorhynchus
anatinus
Monodelphis
domestica
Ailuropoda
melanoleuca
Canis
familiaris
Bos
taurus
Sus
scrofaEquus caballusOryctolagus cuniculusMus musculusRattus norvegicusMacaca mulattaPongo abeliiPan troglodytesHomo sapiensArabidopsis th.0,00180,00260,0011-0,0008-0,00620,0001-0,00020,00150,00230,00200,00130,00230,00200,00210,00180,00170,00170,00200,00160,00200,00200,00190,00190,00190,00180,00190,00180,00180,00190,00190,0019Physcomitrella pat.0,00270,00570,0049-0,0011-0,01280,0011-0,00030,00550,00870,00730,00480,00800,00710,00680,00710,00680,00680,00750,00630,00750,00750,00690,00670,00700,00670,00680,00690,00710,00700,00700,0068Aspergillus niger 0,00170,00330,43300,0019-0,00050,00160,00310,00830,00840,00800,00760,00690,00710,00830,00680,00640,00760,00800,00800,00650,00630,00650,00540,00570,00470,00820,00660,00720,00680,00730,0071Ashbya gossypii0,0008-0,00200,00470,62450,00380,00500,00420,00150,00150,00230,0057-0,0001-0,00060,00130,00080,00070,0001-0,00070,00290,0013-0,0009-0,00230,0002-0,0002-0,00020,00130,0021-0,00030,0017-0,0006-0,0001Saccharomyces c.0,0007-0,0140-0,00120,00250,00440,00150,0012-0,0006-0,0040-0,0027-0,0002-0,0042-0,0039-0,0019-0,0038-0,0020-0,0037-0,0035-0,0031-0,0030-0,0039-0,0049-0,0033-0,0037-0,0038-0,0031-0,0030-0,0037-0,0024-0,0033-0,0036Acyrthosiphon pi.0,0010-0,00040,00660,00590,00200,71800,01490,01070,00350,00480,01070,00260,00330,00560,00320,00360,00420,00470,00680,00400,00270,00240,00390,00360,00430,00460,00380,00280,00360,00250,0034Apis mellifera0,0007-0,00160,00310,00530,00110,01000,73380,0060-0,00030,00140,00850,0014-0,00070,00330,00030,00170,0003-0,00060,00240,00150,0002-0,0023-0,0004-0,0003-0,00140,0025-0,00090,00110,0011-0,0004-0,0002Tribolium castan.0,00180,00500,01050,00220,00030,00870,00590,73370,01570,01430,01390,01550,01600,01370,01470,01300,01290,01350,01380,01520,01420,01410,01480,01370,01510,01600,01380,01450,01500,01460,0147Strongylocentrots p.0,00230,00720,0075-0,0008-0,0034-0,0001-0,00100,01050,70160,02120,01250,01990,01740,01630,01740,01750,01670,01770,01750,02030,01860,01760,01690,01930,01720,01820,01890,01790,01820,01790,0188Saccoglossus kow.0,00200,00610,0071-0,0002-0,00170,00290,00330,00770,01920,66220,00960,01670,01490,01680,01630,01390,01370,01550,01330,01450,01640,01430,01530,01490,01470,01510,01480,01370,01360,01450,0157Ciona intestinalis0,00130,00290,00900,00550,00150,00420,00480,01130,00790,00840,78960,00860,00990,00820,00620,00800,00880,00700,00820,00810,00650,00510,00670,00700,00680,00990,00740,00680,00700,00670,0064Danio rerio0,00210,00630,0055-0,0027-0,00430,0002-0,00300,00910,01890,01720,00880,64890,01640,01630,01740,01550,01670,01630,01390,01610,01670,01600,01610,01680,01400,01490,01670,01550,01750,01830,0154Xenopus tropicalis0,00240,00750,00960,0018-0,00230,00370,00270,01250,02310,02070,01180,02320,66510,02100,02130,02250,02080,02040,01960,02150,02080,02270,02210,02040,01960,02080,01980,02070,02080,02000,0222Anolis carolinensis0,00220,00650,0091-0,0007-0,00180,00370,00320,01130,01980,01690,01230,01780,01910,64770,01810,01760,01980,01700,01570,01980,01700,01820,01830,01990,01870,01940,01890,01740,01810,01810,0179Taeniopygia guttata0,00250,00680,0093-0,0006-0,00200,00210,00180,01380,02170,02040,01200,02190,02200,02020,67300,02850,02670,02190,02010,02210,01990,02160,02090,02010,01740,02020,01980,01930,01970,02080,0201Gallus gallus0,00220,00630,00850,0014-0,00210,00080,00050,00950,02010,01670,01220,01870,01720,01670,02180,67750,04170,01810,01510,01910,01710,01760,01700,01830,01680,01740,01730,01520,01600,01710,0165Meleagris gallopavo 0,00200,00660,00810,0006-0,00240,0013-0,00040,01050,01870,01930,01110,01820,01730,01880,02050,04750,65390,01830,01690,01890,01720,02000,01820,01830,01710,01840,01840,01850,01760,01730,0168Ornithorhynchus a.0,00210,00590,00750,0003-0,00240,00050,00180,00920,02150,01910,01170,02090,01920,01800,01890,01780,01720,65340,02140,02320,02210,02330,02350,02160,01960,02300,02270,01990,01910,02200,0211Monodelphis dom.0,00230,00700,01060,0030-0,00140,00570,00250,01210,02080,02140,01290,02030,01900,01790,02040,02020,02140,02310,66000,02390,02300,02410,02260,02300,02270,02620,02530,02020,02260,02230,0227Ailuropoda melanol.0,00200,00640,00720,0001-0,00360,0023-0,00030,01180,01990,01890,01030,02050,01680,01950,01980,01820,01700,01850,02080,61280,02750,02670,02200,02110,02300,02090,02530,02060,02260,02260,0196Canis familiaris0,00230,00630,00880,0004-0,00290,00020,00170,01040,02140,01980,01170,02140,01870,01910,02020,01870,01970,02390,02050,02740,68510,02880,02670,02670,02350,02820,02680,02280,02330,02520,0249Bos taurus0,00210,00630,00780,0005-0,0028-0,00010,00160,01060,02180,01830,01190,02130,01850,01910,01760,01930,01800,02090,01940,02790,02740,70890,02930,02850,02600,02550,02430,02170,02210,02410,0239Sus scrofa0,00210,00640,00900,0005-0,00260,00090,00160,01200,01820,01670,01190,01960,01820,01860,01590,01780,01720,02000,02020,02470,02440,03110,64580,02740,02750,02200,02600,02000,02220,02240,0200Equus caballus0,00230,00740,0084-0,0007-0,00230,00180,00370,01390,02260,01950,01330,02430,02010,01950,01910,01980,01870,02440,02180,02810,02900,03160,03070,75790,02560,02700,02740,02580,02370,02550,0270Oryctolagus cunic.0,00210,00680,00920,0012-0,00190,00350,00060,00960,02230,01890,01250,02210,01970,01880,01810,01770,01950,02310,02320,02690,02380,02710,02880,02530,68380,02800,02740,02590,02220,02280,0249Mus musculus0,0022
0,0067
0,0106
0,0025
-0,0006
0,0019
0,0041
0,0133
0,0206
0,0183
0,0140
0,0235
0,0183
0,0199
0,0184
0,0204
0,0187
0,0227
0,0231
0,0244
0,0227
0,0275
0,0270
0,0212
0,0240
0,7057
0,0439
0,0241
0,0201
0,0220
0,0233
Rattus
norvegicus
0,0023
0,0063
0,0088
0,0021
-0,0019
0,0023
0,0015
0,0114
0,0211
0,0193
0,0128
0,0198
0,0175
0,0183
0,0201
0,0203
0,0190
0,0216
0,0233
0,0258
0,0242
0,0304
0,0294
0,0242
0,0263
0,0456
0,7398
0,0257
0,0243
0,0262
0,0253
Macaca
mulatta
0,0023
0,0064
0,0092
0,0009
-0,0018
0,0033
0,0021
0,01270,02110,02000,01190,02200,01790,02040,01650,01860,01860,02020,02020,02490,02140,02260,02310,02230,02260,02350,02180,74920,02710,02710,0279Pongo abelii0,00240,00690,00980,0009-0,00130,00410,00580,01260,02140,02150,01330,02290,01950,02160,02000,02130,02060,02170,01990,02470,02120,02360,02590,02310,02330,02340,02640,03170,65080,03980,0416Pan troglodytes0,00230,00670,00840,0007-0,00210,00130,00300,01300,02140,02090,01230,02120,01900,01890,02030,01890,01830,02300,02020,02460,02220,02720,02440,02290,02310,02400,02760,02800,04020,75860,0784Homo sapiens0,00210,00650,0084-0,0005-0,00300,00140,00100,01000,02140,01850,01020,02040,01860,01840,01810,01700,01640,01940,01880,02390,02210,02330,02190,02080,02410,02070,02380,0266
0,0355
0,0741
0,7223
Homininae relationship
Coefficients of similarity
-
0,014 -0,007
-
0,007
-0,003
-
0,003
0,000
0,000 0,003
0,003
0,006
0,006
0,011
0,011
0,016
0,016
0,019
0,019
0,022
0,022
0,025
0,025
0,027
0,027
0,030
0,030
0,040
0,070
0,080Slide31
Results
Arabidopsis
thalianaPhyscomitrella patensAspergillus niger
Ashbya gossypiiSaccharomyces cerevisiaeAcyrthosiphon pisumApis mellifera
Tribolium
castaneumStrongylocentrotus purpuratusSaccoglossus kowalevskiiCiona intestinalisDanio rerioXenopus
(Silurana) tropicalis
Anolis carolinensisTaeniopygia
guttataGallus
gallus
Meleagris
gallopavo
Ornithorhynchus
anatinus
Monodelphis
domestica
Ailuropoda
melanoleuca
Canis
familiaris
Bos
taurus
Sus
scrofaEquus caballusOryctolagus cuniculusMus musculusRattus norvegicusMacaca mulattaPongo abeliiPan troglodytesHomo sapiensArabidopsis th.0,00180,00260,0011-0,0008-0,00620,0001-0,00020,00150,00230,00200,00130,00230,00200,00210,00180,00170,00170,00200,00160,00200,00200,00190,00190,00190,00180,00190,00180,00180,00190,00190,0019Physcomitrella pat.0,00270,00570,0049-0,0011-0,01280,0011-0,00030,00550,00870,00730,00480,00800,00710,00680,00710,00680,00680,00750,00630,00750,00750,00690,00670,00700,00670,00680,00690,00710,00700,00700,0068Aspergillus niger 0,00170,00330,43300,0019-0,00050,00160,00310,00830,00840,00800,00760,00690,00710,00830,00680,00640,00760,00800,00800,00650,00630,00650,00540,00570,00470,00820,00660,00720,00680,00730,0071Ashbya gossypii0,0008-0,00200,00470,62450,00380,00500,00420,00150,00150,00230,0057-0,0001-0,00060,00130,00080,00070,0001-0,00070,00290,0013-0,0009-0,00230,0002-0,0002-0,00020,00130,0021-0,00030,0017-0,0006-0,0001Saccharomyces c.0,0007-0,0140-0,00120,00250,00440,00150,0012-0,0006-0,0040-0,0027-0,0002-0,0042-0,0039-0,0019-0,0038-0,0020-0,0037-0,0035-0,0031-0,0030-0,0039-0,0049-0,0033-0,0037-0,0038-0,0031-0,0030-0,0037-0,0024-0,0033-0,0036Acyrthosiphon pi.0,0010-0,00040,00660,00590,00200,71800,01490,01070,00350,00480,01070,00260,00330,00560,00320,00360,00420,00470,00680,00400,00270,00240,00390,00360,00430,00460,00380,00280,00360,00250,0034Apis mellifera0,0007-0,00160,00310,00530,00110,01000,73380,0060-0,00030,00140,00850,0014-0,00070,00330,00030,00170,0003-0,00060,00240,00150,0002-0,0023-0,0004-0,0003-0,00140,0025-0,00090,00110,0011-0,0004-0,0002Tribolium castan.0,00180,00500,01050,00220,00030,00870,00590,73370,01570,01430,01390,01550,01600,01370,01470,01300,01290,01350,01380,01520,01420,01410,01480,01370,01510,01600,01380,01450,01500,01460,0147Strongylocentrots p.0,00230,00720,0075-0,0008-0,0034-0,0001-0,00100,01050,70160,02120,01250,01990,01740,01630,01740,01750,01670,01770,01750,02030,01860,01760,01690,01930,01720,01820,01890,01790,01820,01790,0188Saccoglossus kow.0,00200,00610,0071-0,0002-0,00170,00290,00330,00770,01920,66220,00960,01670,01490,01680,01630,01390,01370,01550,01330,01450,01640,01430,01530,01490,01470,01510,01480,01370,01360,01450,0157Ciona intestinalis0,00130,00290,00900,00550,00150,00420,00480,01130,00790,00840,78960,00860,00990,00820,00620,00800,00880,00700,00820,00810,00650,00510,00670,00700,00680,00990,00740,00680,00700,00670,0064Danio rerio0,00210,00630,0055-0,0027-0,00430,0002-0,00300,00910,01890,01720,00880,64890,01640,01630,01740,01550,01670,01630,01390,01610,01670,01600,01610,01680,01400,01490,01670,01550,01750,01830,0154Xenopus tropicalis0,00240,00750,00960,0018-0,00230,00370,00270,01250,02310,02070,01180,02320,66510,02100,02130,02250,02080,02040,01960,02150,02080,02270,02210,02040,01960,02080,01980,02070,02080,02000,0222Anolis carolinensis0,00220,00650,0091-0,0007-0,00180,00370,00320,01130,01980,01690,01230,01780,01910,64770,01810,01760,01980,01700,01570,01980,01700,01820,01830,01990,01870,01940,01890,01740,01810,01810,0179Taeniopygia guttata0,00250,00680,0093-0,0006-0,00200,00210,00180,01380,02170,02040,01200,02190,02200,02020,67300,02850,02670,02190,02010,02210,01990,02160,02090,02010,01740,02020,01980,01930,01970,02080,0201Gallus gallus0,00220,00630,00850,0014-0,00210,00080,00050,00950,02010,01670,01220,01870,01720,01670,02180,67750,04170,01810,01510,01910,01710,01760,01700,01830,01680,01740,01730,01520,01600,01710,0165Meleagris gallopavo 0,00200,00660,00810,0006-0,00240,0013-0,00040,01050,01870,01930,01110,01820,01730,01880,02050,04750,65390,01830,01690,01890,01720,02000,01820,01830,01710,01840,01840,01850,01760,01730,0168Ornithorhynchus a.0,00210,00590,00750,0003-0,00240,00050,00180,00920,02150,01910,01170,02090,01920,01800,01890,01780,01720,65340,02140,02320,02210,02330,02350,02160,01960,02300,02270,01990,01910,02200,0211Monodelphis dom.0,00230,00700,01060,0030-0,00140,00570,00250,01210,02080,02140,01290,02030,01900,01790,02040,02020,02140,02310,66000,02390,02300,02410,02260,02300,02270,02620,02530,02020,02260,02230,0227Ailuropoda melanol.0,00200,00640,00720,0001-0,00360,0023-0,00030,01180,01990,01890,01030,02050,01680,01950,01980,01820,01700,01850,02080,61280,02750,02670,02200,02110,02300,02090,02530,02060,02260,02260,0196Canis familiaris0,00230,00630,00880,0004-0,00290,00020,00170,01040,02140,01980,01170,02140,01870,01910,02020,01870,01970,02390,02050,02740,68510,02880,02670,02670,02350,02820,02680,02280,02330,02520,0249Bos taurus0,00210,00630,00780,0005-0,0028-0,00010,00160,01060,02180,01830,01190,02130,01850,01910,01760,01930,01800,02090,01940,02790,02740,70890,02930,02850,02600,02550,02430,02170,02210,02410,0239Sus scrofa0,00210,00640,00900,0005-0,00260,00090,00160,01200,01820,01670,01190,01960,01820,01860,01590,01780,01720,02000,02020,02470,02440,03110,64580,02740,02750,02200,02600,02000,02220,02240,0200Equus caballus0,00230,00740,0084-0,0007-0,00230,00180,00370,01390,02260,01950,01330,02430,02010,01950,01910,01980,01870,02440,02180,02810,02900,03160,03070,75790,02560,02700,02740,02580,02370,02550,0270Oryctolagus cunic.0,00210,00680,00920,0012-0,00190,00350,00060,00960,02230,01890,01250,02210,01970,01880,01810,01770,01950,02310,02320,02690,02380,0271
0,0288
0,0253
0,6838
0,0280
0,0274
0,0259
0,0222
0,0228
0,0249
Mus
musculus
0,0022
0,0067
0,0106
0,0025
-0,0006
0,0019
0,0041
0,0133
0,0206
0,0183
0,0140
0,0235
0,0183
0,0199
0,0184
0,0204
0,0187
0,0227
0,0231
0,0244
0,0227
0,0275
0,0270
0,0212
0,0240
0,7057
0,0439
0,0241
0,0201
0,0220
0,0233
Rattus
norvegicus
0,0023
0,0063
0,0088
0,0021
-0,0019
0,0023
0,0015
0,0114
0,0211
0,0193
0,0128
0,0198
0,0175
0,0183
0,0201
0,0203
0,0190
0,0216
0,0233
0,0258
0,0242
0,0304
0,0294
0,0242
0,0263
0,0456
0,7398
0,0257
0,0243
0,02620,0253Macaca mulatta 0,00230,00640,00920,0009-0,00180,00330,00210,01270,02110,02000,01190,02200,01790,02040,01650,01860,01860,02020,02020,02490,02140,02260,02310,02230,02260,02350,02180,74920,02710,02710,0279Pongo abelii0,00240,00690,00980,0009-0,00130,00410,00580,01260,02140,02150,01330,02290,01950,02160,02000,02130,02060,02170,01990,02470,02120,02360,02590,02310,02330,02340,02640,03170,65080,03980,0416Pan troglodytes0,00230,00670,00840,0007-0,00210,00130,00300,01300,02140,02090,01230,02120,01900,01890,02030,01890,01830,02300,02020,02460,02220,02720,02440,02290,02310,02400,02760,02800,04020,75860,0784Homo sapiens0,00210,00650,0084-0,0005-0,00300,00140,00100,01000,02140,01850,01020,02040,01860,01840,01810,01700,01640,01940,0188
0,0239
0,0221
0,02330,02190,02080,02410,0207
0,02380,02660,03550,07410,7223Coefficients of similarity
-
0,014 -0,007
-
0,007-0,003-0,003 0,0000,000 0,0030,003 0,0060,006 0,0110,011 0,0160,016 0,0190,019 0,0220,022 0,0250,025 0,0270,027 0,0300,030 0,0400,0700,080
Aves
relationshipSlide32
Results
Arabidopsis
thalianaPhyscomitrella patensAspergillus niger
Ashbya gossypiiSaccharomyces cerevisiaeAcyrthosiphon pisumApis mellifera
Tribolium
castaneumStrongylocentrotus purpuratusSaccoglossus kowalevskiiCiona intestinalisDanio rerioXenopus
(Silurana) tropicalis
Anolis carolinensisTaeniopygia
guttataGallus
gallus
Meleagris
gallopavo
Ornithorhynchus
anatinus
Monodelphis
domestica
Ailuropoda
melanoleuca
Canis
familiaris
Bos
taurus
Sus
scrofaEquus caballusOryctolagus cuniculusMus musculusRattus norvegicusMacaca mulattaPongo abeliiPan troglodytesHomo sapiensArabidopsis th.0,00180,00260,0011-0,0008-0,00620,0001-0,00020,00150,00230,00200,00130,00230,00200,00210,00180,00170,00170,00200,00160,00200,00200,00190,00190,00190,00180,00190,00180,00180,00190,00190,0019Physcomitrella pat.0,00270,00570,0049-0,0011-0,01280,0011-0,00030,00550,00870,00730,00480,00800,00710,00680,00710,00680,00680,00750,00630,00750,00750,00690,00670,00700,00670,00680,00690,00710,00700,00700,0068Aspergillus niger 0,00170,00330,43300,0019-0,00050,00160,00310,00830,00840,00800,00760,00690,00710,00830,00680,00640,00760,00800,00800,00650,00630,00650,00540,00570,00470,00820,00660,00720,00680,00730,0071Ashbya gossypii0,0008-0,00200,00470,62450,00380,00500,00420,00150,00150,00230,0057-0,0001-0,00060,00130,00080,00070,0001-0,00070,00290,0013-0,0009-0,00230,0002-0,0002-0,00020,00130,0021-0,00030,0017-0,0006-0,0001Saccharomyces c.0,0007-0,0140-0,00120,00250,00440,00150,0012-0,0006-0,0040-0,0027-0,0002-0,0042-0,0039-0,0019-0,0038-0,0020-0,0037-0,0035-0,0031-0,0030-0,0039-0,0049-0,0033-0,0037-0,0038-0,0031-0,0030-0,0037-0,0024-0,0033-0,0036Acyrthosiphon pi.0,0010-0,00040,00660,00590,00200,71800,01490,01070,00350,00480,01070,00260,00330,00560,00320,00360,00420,00470,00680,00400,00270,00240,00390,00360,00430,00460,00380,00280,00360,00250,0034Apis mellifera0,0007-0,00160,00310,00530,00110,01000,73380,0060-0,00030,00140,00850,0014-0,00070,00330,00030,00170,0003-0,00060,00240,00150,0002-0,0023-0,0004-0,0003-0,00140,0025-0,00090,00110,0011-0,0004-0,0002Tribolium castan.0,00180,00500,01050,00220,00030,00870,00590,73370,01570,01430,01390,01550,01600,01370,01470,01300,01290,01350,01380,01520,01420,01410,01480,01370,01510,01600,01380,01450,01500,01460,0147Strongylocentrots p.0,00230,00720,0075-0,0008-0,0034-0,0001-0,00100,01050,70160,02120,01250,01990,01740,01630,01740,01750,01670,01770,01750,02030,01860,01760,01690,01930,01720,01820,01890,01790,01820,01790,0188Saccoglossus kow.0,00200,00610,0071-0,0002-0,00170,00290,00330,00770,01920,66220,00960,01670,01490,01680,01630,01390,01370,01550,01330,01450,01640,01430,01530,01490,01470,01510,01480,01370,01360,01450,0157Ciona intestinalis0,00130,00290,00900,00550,00150,00420,00480,01130,00790,00840,78960,00860,00990,00820,00620,00800,00880,00700,00820,00810,00650,00510,00670,00700,00680,00990,00740,00680,00700,00670,0064Danio rerio0,00210,00630,0055-0,0027-0,00430,0002-0,00300,00910,01890,01720,00880,64890,01640,01630,01740,01550,01670,01630,01390,01610,01670,01600,01610,01680,01400,01490,01670,01550,01750,01830,0154Xenopus tropicalis0,00240,00750,00960,0018-0,00230,00370,00270,01250,02310,02070,01180,02320,66510,02100,02130,02250,02080,02040,01960,02150,02080,02270,02210,02040,01960,02080,01980,02070,02080,02000,0222Anolis carolinensis0,00220,00650,0091-0,0007-0,00180,00370,00320,01130,01980,01690,01230,01780,01910,64770,01810,01760,01980,01700,01570,01980,01700,01820,01830,01990,01870,01940,01890,01740,01810,01810,0179Taeniopygia guttata0,00250,00680,0093-0,0006-0,00200,00210,00180,01380,02170,02040,01200,02190,02200,02020,67300,02850,02670,02190,02010,02210,01990,02160,02090,02010,01740,02020,01980,01930,01970,02080,0201Gallus gallus0,00220,00630,00850,0014-0,00210,00080,00050,00950,02010,01670,01220,01870,01720,01670,02180,67750,04170,01810,01510,01910,01710,01760,01700,01830,01680,01740,01730,01520,01600,01710,0165Meleagris gallopavo 0,00200,00660,00810,0006-0,00240,0013-0,00040,01050,01870,01930,01110,01820,01730,01880,02050,04750,65390,01830,01690,01890,01720,02000,01820,01830,01710,01840,01840,01850,01760,01730,0168Ornithorhynchus a.0,00210,00590,00750,0003-0,00240,00050,00180,00920,02150,01910,01170,02090,01920,01800,01890,01780,01720,65340,02140,02320,02210,02330,02350,02160,01960,02300,02270,01990,01910,02200,0211Monodelphis dom.0,00230,00700,01060,0030-0,00140,00570,00250,01210,02080,02140,01290,02030,01900,01790,02040,02020,02140,02310,66000,02390,02300,02410,02260,02300,02270,02620,02530,02020,02260,02230,0227Ailuropoda melanol.0,00200,00640,00720,0001-0,00360,0023-0,00030,01180,01990,01890,01030,02050,01680,01950,01980,01820,01700,01850,02080,61280,02750,02670,02200,02110,02300,02090,02530,02060,02260,02260,0196Canis familiaris0,00230,00630,00880,0004-0,00290,00020,00170,01040,02140,01980,01170,02140,01870,01910,02020,01870,01970,02390,02050,02740,68510,02880,02670,02670,02350,02820,02680,02280,02330,02520,0249Bos taurus0,00210,00630,00780,0005-0,0028-0,00010,00160,01060,02180,01830,01190,02130,01850,01910,01760,01930,01800,02090,01940,02790,02740,70890,02930,02850,02600,02550,02430,02170,02210,02410,0239Sus scrofa0,00210,00640,00900,0005-0,00260,00090,00160,01200,01820,01670,01190,01960,01820,01860,01590,01780,01720,02000,02020,02470,02440,03110,64580,02740,02750,02200,02600,02000,02220,02240,0200Equus caballus0,00230,00740,0084-0,0007-0,00230,00180,00370,01390,02260,01950,01330,02430,02010,01950,01910,01980,01870,02440,02180,02810,02900,03160,03070,75790,02560,02700,02740,02580,02370,02550,0270Oryctolagus cunic.0,00210,00680,00920,0012-0,00190,00350,00060,00960,02230,01890,01250,02210,01970,01880,01810,01770,01950,02310,02320,02690,02380,0271
0,0288
0,0253
0,6838
0,0280
0,0274
0,0259
0,0222
0,0228
0,0249
Mus
musculus
0,0022
0,0067
0,0106
0,0025
-0,0006
0,0019
0,0041
0,0133
0,0206
0,0183
0,0140
0,0235
0,0183
0,0199
0,0184
0,0204
0,0187
0,0227
0,0231
0,0244
0,0227
0,0275
0,0270
0,0212
0,0240
0,7057
0,0439
0,0241
0,0201
0,0220
0,0233
Rattus
norvegicus
0,0023
0,0063
0,0088
0,0021
-0,0019
0,0023
0,0015
0,0114
0,0211
0,0193
0,0128
0,0198
0,0175
0,0183
0,0201
0,0203
0,0190
0,0216
0,0233
0,0258
0,0242
0,0304
0,0294
0,0242
0,0263
0,0456
0,7398
0,0257
0,0243
0,02620,0253Macaca mulatta 0,00230,00640,00920,0009-0,00180,00330,00210,01270,02110,02000,01190,02200,01790,02040,01650,01860,01860,02020,02020,02490,02140,02260,02310,02230,02260,02350,02180,74920,02710,02710,0279Pongo abelii0,00240,00690,00980,0009-0,00130,00410,00580,01260,02140,02150,01330,02290,01950,02160,02000,02130,02060,02170,01990,02470,02120,02360,02590,02310,02330,02340,02640,03170,65080,03980,0416Pan troglodytes0,00230,00670,00840,0007-0,00210,00130,00300,01300,02140,02090,01230,02120,01900,01890,02030,01890,01830,02300,02020,02460,02220,02720,02440,02290,02310,02400,02760,02800,04020,75860,0784Homo sapiens0,00210,00650,0084-0,0005-0,00300,00140,00100,01000,02140,01850,01020,02040,01860,01840,01810,01700,01640,01940,0188
0,0239
0,0221
0,02330,02190,02080,0241
0,02070,02380,02660,03550,07410,7223
Insecta
relationship
Coefficients of similarity-0,014 -0,007-0,007-0,003-0,003 0,0000,000 0,0030,003 0,006
0,006
0,011
0,011
0,016
0,016
0,019
0,019
0,022
0,022
0,025
0,025
0,027
0,027
0,030
0,030
0,040
0,070
0,080Slide33
Results
Arabidopsis
thalianaPhyscomitrella patensAspergillus niger
Ashbya gossypiiSaccharomyces cerevisiaeAcyrthosiphon pisumApis mellifera
Tribolium
castaneumStrongylocentrotus purpuratusSaccoglossus kowalevskiiCiona intestinalisDanio rerioXenopus
(Silurana) tropicalis
Anolis carolinensisTaeniopygia
guttataGallus
gallus
Meleagris
gallopavo
Ornithorhynchus
anatinus
Monodelphis
domestica
Ailuropoda
melanoleuca
Canis
familiaris
Bos
taurus
Sus
scrofaEquus caballusOryctolagus cuniculusMus musculusRattus norvegicusMacaca mulattaPongo abeliiPan troglodytesHomo sapiensArabidopsis th.0,00180,00260,0011-0,0008-0,00620,0001-0,00020,00150,00230,00200,00130,00230,00200,00210,00180,00170,00170,00200,00160,00200,00200,00190,00190,00190,00180,00190,00180,00180,00190,00190,0019Physcomitrella pat.0,00270,00570,0049-0,0011-0,01280,0011-0,00030,00550,00870,00730,00480,00800,00710,00680,00710,00680,00680,00750,00630,00750,00750,00690,00670,00700,00670,00680,00690,00710,00700,00700,0068Aspergillus niger 0,00170,00330,43300,0019-0,00050,00160,00310,00830,00840,00800,00760,00690,00710,00830,00680,00640,00760,00800,00800,00650,00630,00650,00540,00570,00470,00820,00660,00720,00680,00730,0071Ashbya gossypii0,0008-0,00200,00470,62450,00380,00500,00420,00150,00150,00230,0057-0,0001-0,00060,00130,00080,00070,0001-0,00070,00290,0013-0,0009-0,00230,0002-0,0002-0,00020,00130,0021-0,00030,0017-0,0006-0,0001Saccharomyces c.0,0007-0,0140-0,00120,00250,00440,00150,0012-0,0006-0,0040-0,0027-0,0002-0,0042-0,0039-0,0019-0,0038-0,0020-0,0037-0,0035-0,0031-0,0030-0,0039-0,0049-0,0033-0,0037-0,0038-0,0031-0,0030-0,0037-0,0024-0,0033-0,0036Acyrthosiphon pi.0,0010-0,00040,00660,00590,00200,71800,01490,01070,00350,00480,01070,00260,00330,00560,00320,00360,00420,00470,00680,00400,00270,00240,00390,00360,00430,00460,00380,00280,00360,00250,0034Apis mellifera0,0007-0,00160,00310,00530,00110,01000,73380,0060-0,00030,00140,00850,0014-0,00070,00330,00030,00170,0003-0,00060,00240,00150,0002-0,0023-0,0004-0,0003-0,00140,0025-0,00090,00110,0011-0,0004-0,0002Tribolium castan.0,00180,00500,01050,00220,00030,00870,00590,73370,01570,01430,01390,01550,01600,01370,01470,01300,01290,01350,01380,01520,01420,01410,01480,01370,01510,01600,01380,01450,01500,01460,0147Strongylocentrots p.0,00230,00720,0075-0,0008-0,0034-0,0001-0,00100,01050,70160,02120,01250,01990,01740,01630,01740,01750,01670,01770,01750,02030,01860,01760,01690,01930,01720,01820,01890,01790,01820,01790,0188Saccoglossus kow.0,00200,00610,0071-0,0002-0,00170,00290,00330,00770,01920,66220,00960,01670,01490,01680,01630,01390,01370,01550,01330,01450,01640,01430,01530,01490,01470,01510,01480,01370,01360,01450,0157Ciona intestinalis0,00130,00290,00900,00550,00150,00420,00480,01130,00790,00840,78960,00860,00990,00820,00620,00800,00880,00700,00820,00810,00650,00510,00670,00700,00680,00990,00740,00680,00700,00670,0064Danio rerio0,00210,00630,0055-0,0027-0,00430,0002-0,00300,00910,01890,01720,00880,64890,01640,01630,01740,01550,01670,01630,01390,01610,01670,01600,01610,01680,01400,01490,01670,01550,01750,01830,0154Xenopus tropicalis0,00240,00750,00960,0018-0,00230,00370,00270,01250,02310,02070,01180,02320,66510,02100,02130,02250,02080,02040,01960,02150,02080,02270,02210,02040,01960,02080,01980,02070,02080,02000,0222Anolis carolinensis0,00220,00650,0091-0,0007-0,00180,00370,00320,01130,01980,01690,01230,01780,01910,64770,01810,01760,01980,01700,01570,01980,01700,01820,01830,01990,01870,01940,01890,01740,01810,01810,0179Taeniopygia guttata0,00250,00680,0093-0,0006-0,00200,00210,00180,01380,02170,02040,01200,02190,02200,02020,67300,02850,02670,02190,02010,02210,01990,02160,02090,02010,01740,02020,01980,01930,01970,02080,0201Gallus gallus0,00220,00630,00850,0014-0,00210,00080,00050,00950,02010,01670,01220,01870,01720,01670,02180,67750,04170,01810,01510,01910,01710,01760,01700,01830,01680,01740,01730,01520,01600,01710,0165Meleagris gallopavo 0,00200,00660,00810,0006-0,00240,0013-0,00040,01050,01870,01930,01110,01820,01730,01880,02050,04750,65390,01830,01690,01890,01720,02000,01820,01830,01710,01840,01840,01850,01760,01730,0168Ornithorhynchus a.0,00210,00590,00750,0003-0,00240,00050,00180,00920,02150,01910,01170,02090,01920,01800,01890,01780,01720,65340,02140,02320,02210,02330,02350,02160,01960,02300,02270,01990,01910,02200,0211Monodelphis dom.0,00230,00700,01060,0030-0,00140,00570,00250,01210,02080,02140,01290,02030,01900,01790,02040,02020,02140,02310,66000,02390,02300,02410,02260,02300,02270,02620,02530,02020,02260,02230,0227Ailuropoda melanol.0,00200,00640,00720,0001-0,00360,0023-0,00030,01180,01990,01890,01030,02050,01680,01950,01980,01820,01700,01850,02080,61280,02750,02670,02200,02110,02300,02090,02530,02060,02260,02260,0196Canis familiaris0,00230,00630,00880,0004-0,00290,00020,00170,01040,02140,01980,01170,02140,01870,01910,02020,01870,01970,02390,02050,02740,68510,02880,02670,02670,02350,02820,02680,02280,02330,02520,0249Bos taurus0,00210,00630,00780,0005-0,0028-0,00010,00160,01060,02180,01830,01190,02130,01850,01910,01760,01930,01800,02090,01940,02790,02740,70890,02930,02850,02600,02550,02430,02170,02210,02410,0239Sus scrofa0,00210,00640,00900,0005-0,00260,00090,00160,01200,01820,01670,01190,01960,01820,01860,01590,01780,01720,02000,02020,02470,02440,03110,64580,02740,02750,02200,02600,0200
0,0222
0,0224
0,0200
Equus
caballus
0,0023
0,0074
0,0084
-0,0007
-0,0023
0,0018
0,0037
0,0139
0,0226
0,0195
0,0133
0,0243
0,0201
0,0195
0,0191
0,0198
0,0187
0,0244
0,0218
0,0281
0,0290
0,0316
0,0307
0,7579
0,0256
0,0270
0,0274
0,0258
0,0237
0,0255
0,0270
Oryctolagus
cunic
.
0,0021
0,0068
0,0092
0,0012
-0,0019
0,0035
0,0006
0,0096
0,0223
0,0189
0,0125
0,0221
0,0197
0,0188
0,0181
0,0177
0,0195
0,0231
0,0232
0,0269
0,0238
0,0271
0,0288
0,0253
0,6838
0,0280
0,0274
0,0259
0,0222
0,0228
0,0249
Mus
musculus
0,00220,00670,01060,0025-0,00060,00190,00410,01330,02060,01830,01400,02350,01830,01990,01840,02040,01870,02270,02310,02440,02270,02750,02700,02120,02400,70570,04390,02410,02010,02200,0233Rattus norvegicus0,00230,00630,00880,0021-0,00190,00230,00150,01140,02110,01930,01280,01980,01750,01830,02010,02030,01900,02160,02330,02580,02420,03040,02940,02420,02630,04560,73980,02570,02430,02620,0253Macaca mulatta 0,00230,00640,00920,0009-0,00180,00330,00210,01270,02110,02000,01190,02200,01790,02040,01650,01860,01860,0202
0,0202
0,0249
0,0214
0,02260,02310,02230,02260,02350,02180,74920,02710,02710,0279
Pongo
abelii
0,00240,00690,00980,0009-0,00130,00410,00580,01260,02140,02150,01330,02290,01950,02160,02000,02130,02060,02170,01990,02470,02120,02360,02590,0231
0,0233
0,0234
0,0264
0,0317
0,6508
0,0398
0,0416Pan troglodytes0,00230,00670,00840,0007-0,00210,00130,00300,01300,02140,02090,01230,02120,01900,01890,02030,01890,01830,02300,02020,02460,02220,02720,02440,02290,02310,02400,02760,02800,04020,75860,0784Homo sapiens0,00210,00650,0084-0,0005-0,00300,00140,00100,01000,02140,01850,01020,02040,01860,01840,01810,01700,01640,01940,01880,02390,02210,02330,02190,02080,02410,02070,02380,02660,03550,07410,7223
Mammalia relationship
Coefficients of similarity
-
0,014 -0,007
-
0,007
-0,003
-
0,003
0,000
0,000 0,003
0,003
0,006
0,006
0,011
0,011
0,016
0,016
0,019
0,019
0,022
0,022
0,025
0,025
0,027
0,027
0,030
0,030
0,040
0,070
0,080Slide34
Results
Arabidopsis
thalianaPhyscomitrella patensAspergillus niger
Ashbya gossypiiSaccharomyces cerevisiaeAcyrthosiphon pisumApis mellifera
Tribolium
castaneumStrongylocentrotus purpuratusSaccoglossus kowalevskiiCiona intestinalisDanio rerioXenopus
(Silurana) tropicalis
Anolis carolinensisTaeniopygia
guttataGallus
gallus
Meleagris
gallopavo
Ornithorhynchus
anatinus
Monodelphis
domestica
Ailuropoda
melanoleuca
Canis
familiaris
Bos
taurus
Sus
scrofaEquus caballusOryctolagus cuniculusMus musculusRattus norvegicusMacaca mulattaPongo abeliiPan troglodytesHomo sapiensArabidopsis th.0,0019Physcomitrella pat.0,0070Aspergillus niger 0,0057Ashbya gossypii-0,0002Saccharomyces c.-0,0037Acyrthosiphon pi.0,0036Apis mellifera-0,0003Tribolium castan.0,0137Strongylocentrots p.0,0193Saccoglossus kow.0,0149Ciona intestinalis0,0070Danio rerio0,0168Xenopus tropicalis0,0204Anolis carolinensis0,0199Taeniopygia guttata0,0201Gallus gallus0,0183Meleagris gallopavo 0,0183Ornithorhynchus a.0,0216Monodelphis dom.0,0230Ailuropoda melanol.0,0211Canis familiaris0,0267Bos taurus0,0285Sus scrofa0,0274Equus caballus0,00230,00740,0084-0,0007-0,00230,00180,00370,01390,02260,01950,01330,02430,02010,01950,01910,01980,01870,02440,02180,02810,02900,03160,03070,75790,02560,02700,02740,02580,02370,02550,0270Oryctolagus cunic.0,0253Mus musculus0,0212Rattus norvegicus0,0242Macaca mulatta 0,0223Pongo abelii
0,0231
Pan
troglodytes
0,0229
Homo sapiens
0,0208
Coefficients of similarity
-
0,014 -0,007
-
0,007
-0,003
-
0,003
0,000
0,000 0,003
0,003
0,006
0,006
0,011
0,011
0,016
0,016
0,019
0,019
0,022
0,022
0,025
0,025
0,027
0,027
0,030
0,030
0,040
0,070
0,080
Imagine
this
is
you
unknown
animalSlide35
Conclusion
Many
mitochondrial
DNA codes were dowloadedThe taxomony relationship between
them
was foundResearch of suitable algorthms for determining the relationship between organisms was doneDemonstrated algorithm was choosenAn algorithm was
implementedAbility to determine the relationship between organisms
using this algorithm was proofedSlide36
Results
Arabidopsis
thalianaPhyscomitrella patensAspergillus niger
Ashbya gossypiiSaccharomyces cerevisiaeAcyrthosiphon pisumApis mellifera
Tribolium
castaneumStrongylocentrotus purpuratusSaccoglossus kowalevskiiCiona intestinalisDanio rerioXenopus
(Silurana) tropicalis
Anolis carolinensisTaeniopygia
guttataGallus
gallus
Meleagris
gallopavo
Ornithorhynchus
anatinus
Monodelphis
domestica
Ailuropoda
melanoleuca
Canis
familiaris
Bos
taurus
Sus
scrofaEquus caballusOryctolagus cuniculusMus musculusRattus norvegicusMacaca mulattaPongo abeliiPan troglodytesHomo sapiensArabidopsis th.0,00180,00260,0011-0,0008-0,00620,0001-0,00020,00150,00230,00200,00130,00230,00200,00210,00180,00170,00170,00200,00160,00200,00200,00190,00190,00190,00180,00190,00180,00180,00190,00190,0019Physcomitrella pat.0,00270,00570,0049-0,0011-0,01280,0011-0,00030,00550,00870,00730,00480,00800,00710,00680,00710,00680,00680,00750,00630,00750,00750,00690,00670,00700,00670,00680,00690,00710,00700,00700,0068Aspergillus niger 0,00170,00330,43300,0019-0,00050,00160,00310,00830,00840,00800,00760,00690,00710,00830,00680,00640,00760,00800,00800,00650,00630,00650,00540,00570,00470,00820,00660,00720,00680,00730,0071Ashbya gossypii0,0008-0,00200,00470,62450,00380,00500,00420,00150,00150,00230,0057-0,0001-0,00060,00130,00080,00070,0001-0,00070,00290,0013-0,0009-0,00230,0002-0,0002-0,00020,00130,0021-0,00030,0017-0,0006-0,0001Saccharomyces c.0,0007-0,0140-0,00120,00250,00440,00150,0012-0,0006-0,0040-0,0027-0,0002-0,0042-0,0039-0,0019-0,0038-0,0020-0,0037-0,0035-0,0031-0,0030-0,0039-0,0049-0,0033-0,0037-0,0038-0,0031-0,0030-0,0037-0,0024-0,0033-0,0036Acyrthosiphon pi.0,0010-0,00040,00660,00590,00200,71800,01490,01070,00350,00480,01070,00260,00330,00560,00320,00360,00420,00470,00680,00400,00270,00240,00390,00360,00430,00460,00380,00280,00360,00250,0034Apis mellifera0,0007-0,00160,00310,00530,00110,01000,73380,0060-0,00030,00140,00850,0014-0,00070,00330,00030,00170,0003-0,00060,00240,00150,0002-0,0023-0,0004-0,0003-0,00140,0025-0,00090,00110,0011-0,0004-0,0002Tribolium castan.0,00180,00500,01050,00220,00030,00870,00590,73370,01570,01430,01390,01550,01600,01370,01470,01300,01290,01350,01380,01520,01420,01410,01480,01370,01510,01600,01380,01450,01500,01460,0147Strongylocentrots p.0,00230,00720,0075-0,0008-0,0034-0,0001-0,00100,01050,70160,02120,01250,01990,01740,01630,01740,01750,01670,01770,01750,02030,01860,01760,01690,01930,01720,01820,01890,01790,01820,01790,0188Saccoglossus kow.0,00200,00610,0071-0,0002-0,00170,00290,00330,00770,01920,66220,00960,01670,01490,01680,01630,01390,01370,01550,01330,01450,01640,01430,01530,01490,01470,01510,01480,01370,01360,01450,0157Ciona intestinalis0,00130,00290,00900,00550,00150,00420,00480,01130,00790,00840,78960,00860,00990,00820,00620,00800,00880,00700,00820,00810,00650,00510,00670,00700,00680,00990,00740,00680,00700,00670,0064Danio rerio0,00210,00630,0055-0,0027-0,00430,0002-0,00300,00910,01890,01720,00880,64890,01640,01630,01740,01550,01670,01630,01390,01610,01670,01600,01610,01680,01400,01490,01670,01550,01750,01830,0154Xenopus tropicalis0,00240,00750,00960,0018-0,00230,00370,00270,01250,02310,02070,01180,02320,66510,02100,02130,02250,02080,02040,01960,02150,02080,02270,02210,02040,01960,02080,01980,02070,02080,02000,0222Anolis carolinensis0,00220,00650,0091-0,0007-0,00180,00370,00320,01130,01980,01690,01230,01780,01910,64770,01810,01760,01980,01700,01570,01980,01700,01820,01830,01990,01870,01940,01890,01740,01810,01810,0179Taeniopygia guttata0,00250,00680,0093-0,0006-0,00200,00210,00180,01380,02170,02040,01200,02190,02200,02020,67300,02850,02670,02190,02010,02210,01990,02160,02090,02010,01740,02020,01980,01930,01970,02080,0201Gallus gallus0,00220,00630,00850,0014-0,00210,00080,00050,00950,02010,01670,01220,01870,01720,01670,02180,67750,04170,01810,01510,01910,01710,01760,01700,01830,01680,01740,01730,01520,01600,01710,0165Meleagris gallopavo 0,00200,00660,00810,0006-0,00240,0013-0,00040,01050,01870,01930,01110,01820,01730,01880,02050,04750,65390,01830,01690,01890,01720,02000,01820,01830,01710,01840,01840,01850,01760,01730,0168Ornithorhynchus a.0,00210,00590,00750,0003-0,00240,00050,00180,00920,02150,01910,01170,02090,01920,01800,01890,01780,01720,65340,02140,02320,02210,02330,02350,02160,01960,02300,02270,01990,01910,02200,0211Monodelphis dom.0,00230,00700,01060,0030-0,00140,00570,00250,01210,02080,02140,01290,02030,01900,01790,02040,02020,02140,02310,66000,02390,02300,02410,02260,02300,02270,02620,02530,02020,02260,02230,0227Ailuropoda melanol.0,00200,00640,00720,0001-0,00360,0023-0,00030,01180,01990,01890,01030,02050,01680,01950,01980,01820,01700,01850,02080,61280,02750,02670,02200,02110,02300,02090,02530,02060,02260,02260,0196Canis familiaris0,00230,00630,00880,0004-0,00290,00020,00170,01040,02140,01980,01170,02140,01870,01910,02020,01870,01970,02390,02050,02740,68510,02880,02670,02670,02350,02820,02680,02280,02330,02520,0249Bos taurus0,00210,00630,00780,0005-0,0028-0,00010,00160,01060,02180,01830,01190,02130,01850,01910,01760,01930,01800,02090,01940,02790,02740,70890,02930,02850,02600,02550,02430,02170,02210,02410,0239Sus scrofa0,00210,00640,00900,0005-0,00260,00090,00160,01200,01820,01670,01190,01960,01820,01860,01590,01780,01720,02000,02020,02470,02440,03110,64580,02740,02750,02200,02600,02000,02220,02240,0200Equus caballus0,00230,00740,0084-0,0007-0,00230,00180,00370,01390,02260,01950,01330,02430,02010,01950,01910,01980,01870,02440,02180,02810,02900,03160,03070,75790,02560,02700,02740,02580,02370,02550,0270Oryctolagus cunic.0,00210,00680,00920,0012-0,00190,00350,00060,00960,02230,01890,01250,02210,01970,01880,01810,01770,01950,02310,02320,02690,02380,02710,02880,02530,68380,02800,02740,02590,02220,02280,0249Mus musculus0,0022
0,0067
0,0106
0,0025
-0,0006
0,0019
0,0041
0,0133
0,0206
0,0183
0,0140
0,0235
0,0183
0,0199
0,0184
0,0204
0,0187
0,0227
0,0231
0,0244
0,0227
0,0275
0,0270
0,0212
0,0240
0,7057
0,0439
0,0241
0,0201
0,0220
0,0233
Rattus
norvegicus
0,0023
0,0063
0,0088
0,0021
-0,0019
0,0023
0,0015
0,0114
0,0211
0,0193
0,0128
0,0198
0,0175
0,0183
0,0201
0,0203
0,0190
0,0216
0,0233
0,0258
0,0242
0,0304
0,0294
0,0242
0,0263
0,0456
0,7398
0,0257
0,0243
0,0262
0,0253
Macaca
mulatta
0,0023
0,0064
0,0092
0,0009
-0,0018
0,0033
0,0021
0,01270,02110,02000,01190,02200,01790,02040,01650,01860,01860,02020,02020,02490,02140,02260,02310,02230,02260,02350,02180,74920,02710,02710,0279Pongo abelii0,00240,00690,00980,0009-0,00130,00410,00580,01260,02140,02150,01330,02290,01950,02160,02000,02130,02060,02170,01990,02470,02120,02360,02590,02310,02330,02340,02640,03170,65080,03980,0416Pan troglodytes0,00230,00670,00840,0007-0,00210,00130,00300,01300,02140,02090,01230,02120,01900,01890,02030,01890,01830,02300,02020,02460,02220,02720,02440,02290,02310,02400,02760,02800,04020,75860,0784Homo sapiens0,00210,00650,0084-0,0005-0,00300,00140,00100,01000,02140,01850,01020,02040,01860,01840,01810,01700,01640,01940,01880,02390,02210,02330,02190,02080,02410,02070,02380,02660,03550,07410,7223
Thank
you
for your attentionCoefficients of similarity
-
0,014 -0,007
-
0,007-0,003-0,003 0,0000,000 0,0030,003 0,0060,006 0,0110,011 0,0160,016 0,0190,019 0,0220,022 0,0250,025 0,0270,027 0,0300,030 0,040
0,070
0,080