Phylogenetic Tree

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Vertebrate topology used at UCSC genome browser

The tree below shows the phylogenetic relationships of vertebrate species with assembled genomes. Lamprey, which recently became available, is not shown but would appear at the bottom as outgroup to all jawed vertebrates.

Adapted from:
28-way vertebrate alignment and conservation track in the UCSC Genome Browser.
Genome Research 17(12):1797-808 Dec 2007
Miller W, ...,Pringle TH, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ.


28wayPhylo.png

Placental mammal phylogenetic tree

Adapted from:
Using genomic data to unravel the root of the placental mammal phylogeny.
Genome Research Apr;17(4):413-21 2007
Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W.

PlacentalTree.png


Alternative topologies for Laurasiatheres

The proper arrangement of species within Laurasiatheres is under active investigation. Two of many alternatives are shown along with L1MA9 retroposon data supporting the Pegasoferae arrangement. Pangolins, not shown and genome project apparently canceled, are now known to be the sister group to carnivores.

LaurasiaAlts.png


Felid phylogeny

Adapted from:
Late Miocene Radiation of Modern Felidae: A Genetic Assessment 
Science Vol. 311 5757 73 - 77 Jan 2006
Johnson WE, Eizirik E, Pecon-Slattery J, Murphy WJ, Antunes A, Teeling E, O'Brien SJ

FelidTree.jpg


Euarchontoglires: rodents, rabbits, primates

Adapted from:
Molecular and genomic data identify the closest living relative of primates.
Science Nov 2;318(5851):792-4 2007
Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann A, Helgen KM, Springer MS, Murphy WJ.

EuarchontaGlires.png

Web tools for drawing phylogenetic trees from Newick format

After grouping the species with nested parentheses (Newick format) that can include divergence dates or substitution rates, the tree can be drawn with various online tools such as phyloGif, Phylodendron, or PhyFi.

Here is a simple example of Newick format: (((((human,chimp),gorilla),orang),gibbon),rhesus);

Two contrasting topologies for Laurasiatheres: (((((dog,cat),horse),(microbat,macrobat)),((((cow,sheep),dolphin),pig),vicugna)),(hedgehog,shrew)); ((((dog,cat),horse),((microbat,macrobat),((((cow,sheep),dolphin),pig),vicugna))),(hedgehog,shrew));

Placental mammals: (((((((((((((+_homSap:5,+_panTro:5):3,-_gorGor:8):3,+_ponPyg:11):14,-_nomLeu:25):10,+_macMul:35):20,+_calJac:55):10,-_tarSyr:65):2,(+_otoGar:58,-_micMur:58):9):10,-_cynVol:77):2,+_tupBel:79):2,((((+_musMus:15,+_ratNor:15):10,+_speTri:25):40,+_cavPor:65):13,+_oryCun:78):3):9,(((((+_canFam:15,+_felCat:15):10,+_equCab:25):20,(+_myoLuc:35,+_pteVam:35):10):20,(+_bosTau:50,+_susScr:50):15):21,(+_sorAra:75,+_eriEur:75):11):4):9,(((+_loxAfr:55, +_proCap:55):37,(-_eleRuf:89, (-_oryAfe:84,+_echTel:84):5):3):5,(+_dasNov:94,(+_choHof:65,-_cycDid:65):29):3):2);

Metazoans: ((((((((((((((((((((((((+_homSap:5,+_panTro:5):3,-_gorGor:8):3,+_ponPyg:11):14,-_nomLeu:25):10,+_macMul:35):20,+_calJac:55):10,-_tarSyr:65):2,(+_otoGar:58,-_micMur:58):9):10,-_cynVol:77):2,+_tupBel:79):2,((((+_musMus:15,+_ratNor:15):10,+_speTri:25):40,+_cavPor:65):13,+_oryCun:78):3):9,(((((+_canFam:15,+_felCat:15):10,+_equCab:25):20,(+_myoLuc:35,+_pteVam:35):10):20,(+_bosTau:50,+_susScr:50):15):21,(+_sorAra:75,+_eriEur:75):11):4):9,(((+_loxAfr:55, +_proCap:55):37,(-_eleRuf:89, (-_oryAfe:84,+_echTel:84):5):3):5,(+_dasNov:94,(+_choHof:65,-_cycDid:65):29):3):2):76, marsupials:175):55,monotremes:230):80,saura:310):90,amphibs:400):50,rayfinned:450):150,jawless:600):50,urochord:650):30,cephalo:680):20,(echino:660,hemi:660):40):100,protostome:800):150,((cnidarian:880,sponge:880):20,placozoa:900):50);

Lesser-known genSpp codes here are thaSir for Thamnophis sirtalis (garter snake) and sphPun for Sphenodon punctatus (tuatura). These species were approved for genome sequencing but to date not begun.

Few people can hand-edit Newick format to include more species or alter relationships. I've developed a linearization of Newick format that puts each species into its own spreadsheet row, separating species and metric data from the "grammar". This allows for easy editing and numerical spreadsheet operations such as to tally up branch lengths in comparative genomics projects. Tabs are ignored by the online tree tools, so the format works by simple paste-in.

									(((((((((((((((((
homSap	:	5							,
panTro	:	5	):	3					,
gorGor	:	8	):	6					,
ponPyg	:	14	):	3					,
nomLeu	:	17	):	8					,
macMul	:	25	):	20					,
calJac	:	45	):	20					,
tarSyr	:	65	):	12					,(
otoGar	:	60							,
micMur	:	60	):	17	):	8			,(
cynVol	:	82							,
tupBel	:	82	):	3	):	2			,((((
musMus	:	16							,
ratNor	:	16	):	53					,
cavPor	:	69	):	9					,(
dipOrd	:	73							,
speTri	:	73	):	5	):	4			,(
ochPri	:	80							,
oryCun	:	80	):	2	):	5	):	8	,((((((
canFam	:	54							,
felCat	:	54	):	8					,
manPen	:	62	):	11					,
equCab	:	73	):	7					,(
myoLuc	:	69							,
pteVam	:	69	):	11	):	7			,(((
turTru	:	53							,
bosTau	:	53	):	8					,
susScr	:	61	):	12					,
vicPac	:	73	):	14	):	4			,(
eriEur	:	80							,
sorAra	:	80	):	11	):	4	):	3	,((
dasNov	:	65							,
choHof	:	65	):	27					,((
loxAfr	:	59							,
proCap	:	59	):	16					,
echTel	:	75	):	17	):	6	):	27	,(
monDom	:	45							,
macEug	:	45	):	80			):	50	,
ornAna	:	175					):	135	,(((
galGal	:	218							,
taeGut	:	218	):	57					,
droNov	:	275	):	23					,
allMis	:	298	):	12	):	5			,((
anoCar	:	250							,
thaSir	:	250	):	50					,
sphPun	:	300	):	15	):	5			,
xenTro	:	320					):	3	

The UCSC 100-way vertebrate genome phylogenetic tree in Newick format

Either of the two representations of the vertebrate genome phylogenetic tree, when pasted into the UCSC tree drawing utility phyloGif, will reproduce species relatedness used at UCSC tracks and resources. Note coding genes are given for the 100-way in the order listed (see proteinFasta on gene details page) as both nucleotide and amino acid exonic format.

The first representation shows various higher order tax as individual lines, for example great apes as the first line. (Line returns are not part of Newick format but are generally ignored by drawing tools.) This display makes it slightly easier to add new species. Thus, to add echidna (Tachyglossus aculeatus), the monotreme line can be hand-edited: ornAna), --> (tacAcu,ornAna), as this genome becomes available.

The second representation is linearized to spreadsheet format. This separates the genus species list from parenthetic nesting used to describe topology. Branching times (or evolutionary rates) can be taken from the literature and can be inserted (as shown above) to draw trees whose horizontal lines have quantitative significance.

The graphic shows an advanced use of the linearized format. The 100-way and Blast searches were used to obtain 100 orthologs of the opsin gene ONP5 (neuropsin). Position 168 was then extracted from the protein alignment and its value placed in front of the appropriate species, followed by an underscore (_) which is interpeted as a space by phyloGif.

The display was then colored to illustrate that a shift from alanine to threonine occurred at the divergence of placental mammals from marsupials. Alanine was ancestral in deuterostomes and continues to this day to be invariant in non-placentals. The threonine substitution for its part came under strong selection too and has been invariant over several billion years of summed placental branch length. Such substitutions are called phyloSNPs or phylogenetically coherent events.

((((((((((((((((((homSap,panTro),gorGor),ponAbe),nomLeu),
(((rheMac,macFas),papHam),chlSab)),
(calJac,saiBol)),otoGar),tupChi),
(((speTri,(jacJac,((micOch,(criGri,mesAur)),(musMus,ratNor)))),
(hetGla,(cavPor,(chiLan,octDeg)))),
(oryCun,ochPri))),
((susScr,((vicPac,camFer),((turTru,orcOrc),(panHod,(bosTau,(oviAri,capHir)))))),
((((equCab,cerSim),
(felCat,(canFam,(musFur,(ailMel,(odoRos,lepWed)))))),
((pteAle,pteVam),((myoDav,myoLuc),eptFus))),
(eriEur,(sorAra,conCri))))),
(((((loxAfr,eleEdw),triMan),(chrAsi,echTel)),oryAfe),dasNov)),
(monDom,(sarHar,macEug))),
ornAna),
(((((((falChe,falPer),(((ficAlb,((zonAlb,geoFor),taeGut)),pseHum),(melUnd,(amaVit,araMac)))),colLiv),(anaPla,(galGal,melGal))),
allMis),
((cheMyd,chrPic),(pelSin,apaSpi))),
anoCar)),
xenTro),
latCha),
(((((((tetNig,(takRub,takFla)),(oreNil,(neoBri,(hapBur,(mayZeb,punNye))))),(oryLat,xipMac)),gasAcu),gadMor),(danRer,astMex)),
lepOcu)),
petMar);
	((((((((((((((((((
homSap	,
panTro	),
gorGor	),
ponAbe	),
nomLeu	),(((
rheMac	,
macFas	),
papHam	),
chlSab	)),(
calJac	,
saiBol	)),
otoGar	),
tupChi	),(((
speTri	,(
jacJac	,((
micOch	,(
criGri	,
mesAur	)),(
musMus	,
ratNor	)))),(
hetGla	,(
cavPor	,(
chiLan	,
octDeg	)))),(
oryCun	,
ochPri	))),((
susScr	,((
vicPac	,
camFer	),((
turTru	,
orcOrc	),(
panHod	,(
bosTau	,(
oviAri	,
capHir	)))))),((((
equCab	,
cerSim	),(
felCat	,(
canFam	,(
musFur	,(
ailMel	,(
odoRos	,
lepWed	)))))),((
pteAle	,
pteVam	),((
myoDav	,
myoLuc	),
eptFus	))),(
eriEur	,(
sorAra	,
conCri	))))),(((((
loxAfr	,
eleEdw	),
triMan	),(
chrAsi	,
echTel	)),
oryAfe	),
dasNov	)),(
monDom	,(
sarHar	,
macEug	))),
ornAna	),(((((((
falChe	,
falPer	),(((
ficAlb	,((
zonAlb	,
geoFor	),
taeGut	)),
pseHum	),(
melUnd	,(
amaVit	,
araMac	)))),
colLiv	),(
anaPla	,(
galGal	,
melGal	))),
allMis	),((
cheMyd	,
chrPic	),(
pelSin	,
apaSpi	))),
anoCar	)),
xenTro	),
latCha	),(((((((
tetNig	,(
takRub	,
takFla	)),(
oreNil	,(
neoBri	,(
hapBur	,(
mayZeb	,
punNye	))))),(
oryLat	,
xipMac	)),
gasAcu	),
gadMor	),(
danRer	,
astMex	)),
lepOcu	)),
petMar	)

Neur1MarsupPlacent2.png

Available genome assemblies as of May 2008

The table is correct as of 01 May 08. The species are listed in quasi phylogenetic order (with human arbitrarily listed first and other subtree ordered by genome quality).

  • Traces indicated in millions, eg Trc12 means 12 million traces but no wgs contigs or assembly available
  • Wgs08 means wgs division of GenBank contains short assembled contigs searchable with tBlastn
  • Mar06 etc means the March 2006 assembly is the most recent available at UCSC
Mar06  homSap  Homo  sapiens  (human)
Mar06  panTro  Pan  troglodytes  (chimp)
Trc04  gorGor  Gorilla  gorilla  (gorilla)
Jul07  ponPyg  Pongo  pygmaeus  (orang_abelii)
Trc19  nomLeu  Nomascus  leucogenys  (gibbon)
Jan06  macMul  Macaca  mulatta  (rhesus)
Trc12  papHam  Papio  hamadryas  (baboon)
Trc17  tarSyr  Tarsius  syrichta  (tarsier)
Jun07  calJac  Callithrix  jacchus  (marmoset)
Dec06  otoGar  Otolemur  garnettii  (bushbaby)
Wgs08  micMur  Microcebus  murinus  (mouse_lemur)
Trc00  cynVol  Cynocephalus  volans  (flying_lemur)
Dec06  tupBel  Tupaia  belangeri  (treeshrew)
Jul07  musMus  Mus  musculus  (mouse)
Nov04  ratNor  Rattus  norvegicus  (rat)
Wgs08  speTri  Spermophilus  tridecemlineatus  (ground_squirrel)
Trc07  dipOrd  Dipodomys  ordii  (kangaroo_rat)
Wgs08  cavPor  Cavia  porcellus  (guinea_pig)
May05  oryCun  Oryctolagus  cuniculus  (rabbit)
Wgs08  ochPri  Ochotona  princeps  (pika)
May05  canFam  Canis  familiaris  (dog)
Mar06  felCat  Felis  catus  (cat)
Jan07  equCab  Equus  caballus  (horse)
Wgs08  myoLuc  Myotis  lucifugus  (microbat)
Trc08  pteVam  Pteropus  vampyrus  (macrobat)
Aug06  bosTau  Bos  taurus  (cow)
Trc10  turTru  Tursiops  truncatus  (dolphin)
Trc06  susScr  Sus  scrofa  (pig)
Trc11  vicVic  Vicugna  vicugna  (vicugna)
Wgs08  sorAra  Sorex  araneus  (shrew)
Wgs08  eriEur  Erinaceus  europaeus  (hedgehog)
May05  loxAfr  Loxodonta  africana  (elephant)
Trc09  proCap  Procavia  capensis  (hyrax)
Jul05  echTel  Echinops  telfairi  (tenrec)
May05  dasNov  Dasypus  novemcinctus  (armadillo)
Trc09  choHof  Choloepus  hoffmanni  (sloth)
Jan06  monDom  Monodelphis  domestica  (opossum)</span>
Trc10  macEug  Macropus  eugenii  (wallaby)
Mar07  ornAna  Ornithorhynchus  anatinus  (platypus)
May06  galGal  Gallus  gallus  (chicken)
Trc15  taeGut  Taeniopygia  guttata  (finch)
Feb07  anoCar  Anolis  carolinensis  (lizard)
Aug05  xenTro  Xenopus  tropicalis  (frog)
Jul07  danRer  Danio  rerio  (zebrafish)
Feb04  tetNig  Tetraodon  nigroviridis  (pufferfish)
Oct04  takRub  Takifugu  rubripes  (fugu)
Feb06  gasAcu  Gasterosteus  aculeatus  (stickleback)
Apr06  oryLat  Oryzias  latipes  (medaka)
Wgs08  calMil  Callorhinchus  milii  (elephantfish)
Mar07  petMar  Petromyzon  marinus  (lamprey)

Genus and species commonly used in comparative genomics

The list below provides correctly spelled genus and species for which complete genes are commonly available, either from whole genome sequencing, large-scale cDNA projects, or transcriptome sets.

To align a set orthologous genes collected for a specific comparative project, replace the word 'gene' with its HUGO acronym (example PRNP). Then replace the '.' and the spaces with tabs and paste into spreadsheet columns. Then add accession numbers, taxon ID and sequence data to new columns. Replace the final ')' with a ')lineReturn' converts to standard fasta format. (Note the fasta header here is a database in its own right.)

The first column of numbers then sort the rows into the same anthropocentric order of species as seen in the 100-species alignment at the UCSC human genome browser which is the same order as in the 100-way download page at proteinFasta link from the gene details page.

The second column of numbers will sort rows into quasi-phylogenetic ordering (human taken arbitrarily as first). They're in that order now, but some important web alignment tools do not have an option to retain input order, meaning that phylogenetic ordering needs to be restored after the alignment for purposes of comparative genomics.

>10.10.gene_homSap Homo sapiens (human)
>11.11.gene_panTro Pan troglodytes (chimp)
>99.12.gene_gorGor Gorilla gorilla (gorilla)
>99.13.gene_ponPyg Pongo pygmaeus (orang_sumatran)
>99.14.gene_nomLeu Nomascus leucogenys (gibbon)
>12.15.gene_macMul Macaca mulatta (rhesus)
>12.15.gene_macFas Macaca fascicularis (crab-eating macaque)
>12.15.gene_macNem Macaca nemestrina (pig-tailed macaque)
>99.16.gene_papAnu Papio anubis (baboon)
>99.17.gene_papHam Papio hamadryas (baboon)
>99.18.gene_calJac Callithrix jacchus (marmoset)
>99.19.gene_tarSyr Tarsius syrichta (tarsier)
>13.20.gene_otoGar Otolemur garnettii (bushbaby)
>99.21.gene_micMur Microcebus murinus (mouse_lemur)
>99.22.gene_cynVol Cynocephalus volans (flying_lemur)
>14.23.gene_tupBel Tupaia belangeri (tree_shrew)
>15.24.gene_musMus Mus musculus (mouse)
>16.25.gene_ratNor Rattus norvegicus (rat)
>17.26.gene_cavPor Cavia porcellus (guinea_pig)
>99.27.gene_speTri Spermophilus tridecemlineatus (squirrel)
>99.28.gene_dipOrd Dipodomys ordii (kangaroo_rat)
>18.29.gene_oryCun Oryctolagus cuniculus (rabbit)
>99.30.gene_ochPri Ochotona princeps (pika)
>21.31.gene_canFam Canis familiaris (dog)
>22.32.gene_felCat Felis catus (cat)
>23.36.gene_equCab Equus caballus (horse)
>99.37.gene_myoLuc Myotis lucifugus (microbat)
>99.38.gene_pteVam Pteropus vampyrus (macrobat)
>99.39.gene_turTru Tursiops truncatus (dolphin)
>24.33.gene_bosTau Bos taurus (cow)
>99.34.gene_oviAri Ovis aries (sheep)
>99.35.gene_susScr Sus scrofa (pig)
>99.41.gene_vicVic Vicugna vicugna (vicugna)
>19.42.gene_eriEur Erinaceus europaeus (hedgehog)
>20.43.gene_sorAra Sorex araneus (shrew)
>99.44.gene_borAnc Boreoeuthere ancestralis (ancestral)
>25.45.gene_dasNov Dasypus novemcinctus (armadillo)
>99.46.gene_choHof Choloepus hoffmanni (sloth)
>26.47.gene_loxAfr Loxodonta africana (elephant)
>99.48.gene_proCap Procavia capensis (hyrax)
>99.49.gene_echTel Echinops telfairi (tenrec)
>27.50.gene_monDom Monodelphis domestica (opossum)
>99.51.gene_macEug Macropus eugenii (wallaby)
>99.52.gene_triVul Trichosurus vulpecula (possum)
>28.53.gene_ornAna Ornithorhynchus anatinus (platypus)
>99.54.gene_tacAcu Tachyglossus aculeatus (echidna)
>30.55.gene_galGal Gallus gallus (chicken)
>99.56.gene_taeGut Taeniopygia guttata (finch)
>29.57.gene_anoCar Anolis carolinensis (lizard)
>31.58.gene_xenTro Xenopus tropicalis (frog)
>99.59.gene_xenTro Xenopus laevis (frog)
>99.60.gene_neoFor Neoceratodus forsteri (lungfish)
>32.61.gene_danRer Danio rerio (zebrafish)
>33.62.gene_tetNig Tetraodon nigroviridis (pufferfish)
>34.63.gene_takRub Takifugu rubripes (fugu)
>35.64.gene_gasAcu Gasterosteus  aculeatus (stickleback)
>36.65.gene_oryLap Oryzias latipes (medaka)
>99.66.gene_ictPun Ictalurus punctatus (fish)
>99.67.gene_oncMyk Oncorhynchus mykiss (trout)
>99.68.gene_funHet Fundulus heteroclitis (flounder)
>99.69.gene_calMil Callorhinchus milii (elephantfish)
>99.70.gene_squAca Squalus acanthias (spiny dogfish)
>99.71.gene_petMar Petromyzon marinus (lamprey)
>99.72.gene_braFlo Branchiostoma floridae (amphioxus)
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