iPlant TNRS presentation for phylotatsic

1. iPlant's
Taxonomic
Name
Resolu3on
Service
Naim
Matasci
BIO5
/
The
iPlant
Collabora3ve

2. Ancestral
state
of
Hawaiian
lobelioids
Lobelia
niihauensis
(Image:
David
Eickhoff)
Cyanea
leptostegia
(Image:
Karl
Magnacca)

4. Con3nuous
Ancestral
Character
Es3ma3on
?
(Schulter
et
al.
1997,
Paradis
2004)

5. Obtain
Align
Build
Tree
sequences
sequences
• FastTree
• GetSeq
• Muscle
(aML)
• Ninja
(NJ)
• PHYLIP
(MP,
NJ,
ML)
• RAxML
(ML)
Visualize
Integrate
Run
Analysis
Tree
Data
• CACE
• iPlant
• Lopper
• DACE
Tree
• TNRS
• Contrast
Viewer
• OUch
• Picante
• Penalized
likelihood

6. Obstacles
!"#$%&'()'*'$+,&,
!"#$%&'(-&%%",'
!"#$%&'(.%"/&'01"+2&,
3/$1'2"%"#$%&'()'*'&$+,&,
3/$1'2"%"#$%&'(1'4/",2'456,
!"#$%&'(567"%$*4'
!"#$%&'(6*44"&8$,
!"#$%&'(+&&5'*$+,&,
9/&.5'1&'(&+,&.+&,
9/&.5'1&'(/"4)&&
:$%&,,$'(/562&8",7$/1'
:$%&,,$'(,*#4"/8'2'
;6'+$'(7&%",'
;6'+$'('4*1&+'2'
;6'+$'(5&/2$%%'
;6'+$'(4"/&'4$'
;6'+$'(%$72",2$.&'
;%$/1"+2&'()')$'+'
;%$/1"+2&'(7'/-&<%"/'
;%$/1"+2&'('/#"/$,4$+,
;%$/1"+2&'(<'*/&$&
Number
of
taxa
Taxa
names

7. Taxonomic
uncertainty
1. Non-­‐existent
names
• Misspellings
• Contamina3on
• Annota3ons
• Morphospecies
• Digi3za3on
issues
(frame
shi[s,
character
encoding)
Lexical
variants
(digi3za3on
conven3ons)
2. Synonymy
• Nomenclatural
synonyms
• Taxonomic
synonyms
/
concepts
3. Misiden3fica3ons,
incomplete
iden3fica3ons

8. a)
Centaurium
curvistamineum
(Wi`r.)
Abrams
(1951)
b)
Centaurium
minimum
(Howell)
Piper
(1915)
c)
Centaurium
muhlenbergii
(Griseb.)
Wight
ex
Piper
(1906)
d)
Centaurium
muhlenbergii
(Griseb.)
Wight
ex
Piper
forma
albiflorum
(Suksd.)
St.
John
(1937)
e)
Centaurium
muhlenbergii
(Griseb.)
Wight
ex
Piper
var.
albiflorum
Suksd.
(1927)
f)
Centaurodes
muhlenbergii
(Griseb.)
Kuntze
(1891)
g)
Erythraea
curvistaminea
Wi`r.
(1886)
h)
Erythraea
minima
Howell
(1901)
i)
Erythraea
muhlenbergii
Griseb.
(1839)
Image:
Gordon
Leppig
&
Andrea
J.
Pickart

9. How
to
figure
that
out?
…or
ask
around
at
My-­‐Plant.org

10. Original
Use
Case
–
Density
Plots
(BIEN/NCEAS)
Makemake
at
de.wikipedia

11. Hans
Hillewaert

12. Taxonomic
Name
Resolu3on
Service
• Computer
assisted
standardiza3on
of
plant
names
• Corrects
spelling
errors
and
alterna3ve
spellings
to
a
standard
list
of
names
• Convert
out-­‐of-­‐date
names
to
currently
accepted
names

16. Lobelia
kauaensis
Lobelia
villosa
Galeatella
gloria-­‐mon3s
Trematolobelia
kauaiensis
Trematolobelia
macrostachys
Lobelia
hypoleuca
Neowimmeria
yuccoides
Lobelia
niihauensis
Brighamia
insignis
Brighamia
rockii
Delissea
rhy3dosperma
Delissea
subcordata
Cyanea
acuminata
Cyanea
hirtella
Cyanea
coriacea
Delissea
leptostegia
Clermon3a
kakeana
Clermon3a
parviflora
Clermon3a
arborescens
Clermon3a
fauriei

17. Obtain
Align
Build
Tree
sequences
sequences
• FastTree
• GetSeq
• Muscle
(aML)
• Ninja
(NJ)
• PHYLIP
(MP,
NJ,
ML)
• RAxML
(ML)
Visualize
Integrate
Run
Analysis
Tree
Data
• CACE
• iPlant
• Lopper
• DACE
Tree
• TNRS
• Contrast
Viewer
• OUch
• Picante
• Penalized
likelihood

18. maxHeight.m
14
12 1.000 ●Lobelia kauaensis
●
10 ●Lobelia villosa
8 0.426 ●Lobelia niihauensis
0.937 ●
6 ● 0.977 ●Galeatella gloria montis
●
4 1.000 ●Neowimmeria yuccoides
2
●
0.757 ●Lobelia hypoleuca
0
●
●Trematolobelia macrostachys
0.986
●0.931 ●Delissea subcordata
●
0.970
● ●Delissea rhytidosperma
●Brighamia insignis
0.822
● 0.992 ●Cyanea coriacea
●
●Delissea leptostegia
0.750
0.839 ●Clermontia parviflora
● ●
0.959
● ●Clermontia kakeana
0.993
0.996
● ●Clermontia arborescens
●
●Clermontia fauriei
0.881
● 0.958 ●Cyanea acuminata
●
0.454 ●Cyanea hirtella
●
●Brighamia rockii
●Trematolobelia kauaiensis

24. Issues
• Plants
only
–
cross-­‐code
homonyms
• Lexical
reconcilia3on
– Chondodendron
tomentosum
R.
P.
aff.
=
Chondodendron
tomentosum
Ruiz
&
Pav.
• API
• Performance
(caching)