Download Resolving the Phylogenetic Position of Coelacanth: The Closest

ResolvingthePhylogeneticPositionofCoelacanth:TheClosest
RelativeIsNotAlwaystheMostAppropriateOutgroup
Takezaki N,NishiharaH.2016.GenomeBiol Evol 8:1208-1221.
Abstract
Determiningthephylogeneticrelationshipoftwoextantlineagesoflobe-finnedfish,coelacanths
andlungfishes,andtetrapods isimportantforunderstandingtheoriginoftetrapods.Weanalyzed
datasetsfromtwopreviousstudiesalongwithanewlycollecteddataset,eachofwhichhad
varyingnumbersofspeciesandgenesandvaryingextentofmissingsites.Wefoundthatinallthe
datasetsthesisterrelationshipoflungfishandtetrapods wasconstructedwiththeuseof
cartilaginousfishastheoutgroupwithahighdegreeofstatisticalsupport.Incontrast,whenrayfinnedfishwereusedastheoutgroup,whichistaxonomicallyanimmediateoutgroupoflobefinnedfishandtetrapods,thesisterrelationshipofcoelacanthandtetrapods wassupportedmost
strongly,althoughthestatisticalsupportwasweaker.Eventhoughitisgenerallyacceptedthatthe
closestrelativeisanappropriateoutgroup,ouranalysissuggestedthatthelargedivergenceofthe
ray-finnedfishasindicatedbytheirlongbranchlengthsanddifferentaminoacidfrequenciesmade
themlesssuitableasanoutgroupthancartilaginousfish.
a)
Lobe-finned
vertebrate
Bony vertebrates
Ray-finned fish
Cartilaginous fish
b)
Tree 1
Tetrapod
Lungfish
Coelacanth
Ray-finned fish
Tetrapod
Tree 2
Coelacanth
Lungfish
Ray-finned fish
Tetrapod
Tree 3
Coelacanth
Lungfish
Ray-finned fish
Fig.1.—Thephylogeneticrelationshipofthemajorlineagesinjawedvertebratesandlobe-finned
vertebrates.(a)Therelationshipofmajorlineagesinjawedvertebrates.(b)Threepossible
relationshipsforthethreeextantlineagesoflobe-finnedvertebrates:sisterrelationshipsoflungfishes
andtetrapods (Tree1),coelacanthsandtetrapods (Tree2)andlungfishesandcoelacanths(Tree3).
Table1
DatasetsAnalyzedinThisStudy
Note.—IndatasetI,onlyconcatenatedsequencewasavailable,andtwosharkspecieswere
missing.IndatasetIIgeneswith<50aminoacidsiteswereexcluded.
Missingsites
Dataset
Source
I
Amemiyaetal.
II
Liangetal.
III
Thisstudy
Genes
Aminoacidsites
(%)
Species
251
112,212
20
14.2
1,288
618,946
10
6.5
831
242,475
25
0
a)
Human
Mouse
54
0.05
Dog
100
Armadillo
100
Elephant
Tammar wallaby
100
100
Opossum
Platypus
100
100 Chicken
100
Turkey
100
Zebra finch
100
Lizard
Western clawed frog
100
Chinese brown frog
Lungfish
Coelacanth
Tilapia
100
Pufferfish
100
Zebrafish
Little skate
99
99
87
97
b)
Human
Chicken
100
100
100
100
Western clawed frog
Lungfish
Coelacanth
Pufferfish
100
100
100
d)
Human
Mouse
Dog
Armadillo
100
Elephant
Tammar wallaby
100
100
Opossum
Platypus
100
100 Chicken
100
Turkey
Zebra finch
100
Lizard
Western clawed frog
100
Chinese brown frog
Coelacanth
Lungfish
Tilapia
100
Pufferfish
100
Zebrafish
99
99
59
100
0.05
100
54
e)
100
100
0.05
Human
Chicken
95
Western clawed frog
Coelacanth
Lungfish
Zebrafish
Spotted catshark
Little skate
Pufferfish
100
Zebrafish
Elephant shark
0.05
Human
Mouse
Dog
Elephant
100
77
Armadillo
0.05
Tasmanian devil
100
Opossum
100 Chicken
100
100
Turkey
100
Duck
100
100
Flycatcher
Turtle
100
100
Lizard
Western clawed frog
100
Lungfish
Coelacanth
Platyfish
100
100
Medaka
Tilapia
100
Stickleback
100
Pufferfish
79
Cod
100
Zebrafish
Spotted catshark
100
Little skate
100
Elephant shark
c)
100
100
100
f)
Human
Mouse
Dog
100
Elephant
100
Armadillo
73
Tasmanian devil
100
Opossum
100
100 Chicken
100
Turkey
100
Duck
100
Flycatcher
Turtle
100
Lizard
Western clawed frog
Coelacanth
Lungfish
100
Platyfish
100
Medaka
100
Tilapia
Stickleback
100
95
Pufferfish
Cod
Zebrafish
100
100
0.05
100
52
100
Fig. 2.—Maximum likelihood trees constructed for concatenated sequences of the three datasets. (a)–
(c): CF and RF were used as the outgroup. (d)–(f): RF were used as the outgroup. (a), (d): Dataset I
from Amemiya et al. (2013). (b), (e): Dataset II from Liang et al. (2013). (c), (f): Dataset III collected
in this study. The numbers on the branches are BPs from 500 replications. The trees were constructed
with the JTTFG4 setting by PhyML.