Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales 1

33 Pages·2010·28.3 MB·English

by  Thomas J Givnish

ASSEMBLING THE TREE OF THE
Thomas Gwnish? Mercedes Arm,
J.
MONOCOTYLEDONS: PLASTOME
1 1
i . i i
PHYLOGENY AND
SEQUENCE
EVOLUTION OF POALES
1
Wendy Zo Melvin
B. G. Briggs,*
9 10
R. Duvall, Michael Moore, Michael
J. J.
11
Heaney, Douglas
E.
Soltis,
Kevin 13 and James H. Leebens-Mack3
Thiele,
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ommelinid
orders with n
i (
allies) are well supported as siste a xyrid clade (Erioc
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Bot. Card. 97: 584-616. Published on 27 December 2010.
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Key words: Commelinids,
—
Monocots V
with
ca.
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Phylogen
>erm
onships each other that remain
to
most dherse, inn ried, ecologically included the validation, to a large degree,
economically
ind
i
angio<-permr.. Since l"l
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ill
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/
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li-; ...'.?;
ill
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2000, 2006; Zomlefer, 195
ia, b,
of the aquatic
la
ma
1976; Dahlgren
a n IN, mm. et al.,
i I !l li urn l i ill i I I ill I 111 I I III II III i I
I I
evolutionary biologists. ::
:
:
Over the past 18 years, molecular systematics has
!'
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2000, 2006;
b, \-. ::" -v-v "., -
i nil i li i II in ill v. ' ';.
I
l: .:i ;i .<!..
.™
1999, 2005; Brem 2001;
s et al.,
Chase provided the most powerful
et al. (2006)
.:;
,< ll'i; 'i-iii; :'.,
II
parsimonj (MP)
analysis,
other
ster to all
in,
. .
lid clade (Chase et al, 1993, 1995a)
and on Chase
their
allies). et al.
!i':i
' ' ' ' ' ri,...:l .::
2009, here reco ships within orders
),

nmelmid-
plastid genes (rbcL and nuitK) for repieM and \spar-
n'
.
i i I
ca. 2400 monoeot geneui. he-e efloit- aie eomple- .juenced included members of
I >
while the Europeans link our backbone phylogeny to .-'iigle lamilies in
We
Arecales and Dasypogonales (Dasypogonaceae sensu
are jImi ollabo-
.a.
c
Angiosperm Phylogeny Group, Nonmonocot
w 2009).
We
sendix used
1).
amount
leled of gr
AToL Moore
plant genomes obtained in our projecl et al., 2007; et al, 2007) as
- ' er>''
'!-
' i ' '
:
any major plant group studied to date.
we
In this paper, present a demonstration of the plastome SEQUENCING
focusing on
relali,
Following methods described by Jansen
e ies
«
Poales
is Lh ' -
Ho.sta Tratt.,
I,.,
quenceofitsinelu
....II '
I.
I '
. .
vere generated
De
each novo assemblies sequences
for taxon. of
ip
1 i
:,
-lei
:'
I
2004). Resulting assemblies were
in
Consed (Gordon an
et al, 1998)
The 83 taxa include. were anno-
3S
Group (Appendix
(2009) 1). U ;rver (<http://
.;
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.
HI
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(Ratan, 2009;
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and
available (Edgar, 2004), to
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concatenated alignment.
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closel) rela
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genome
sequences were used as alternative references v>'- Ms-
1.
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Gapped were
cells treated as missing c1
tated and extracted from the resulting contigs using lands of equally most parsimonious trees
DOGMA. DOG\l BLASTX searches seeded
through
o acid sequences iploying tree
sequencing
rare
i t i . . I " . '
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In..
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il>i
... ihli-lllll
! ir i. ii:'
.
&
homoplas) in the data (Givnish Sytsma, 1997).
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IIMili'- -I. '•
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A
was modeled
2004). single; as
i
ii!
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was modeled
using the discrete
a
&
Ucata (Hook, Newell B. C. Stone
f.)
mry direct sequencing. All gene
.
-
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with a total of
}
! .'.i:;i
i'.)
,ii
&
son Maddison, 1992)
to infer an.-.
n
i
we
ecologies, separated
-Live
i
n ii I
and sampled
alignn (a suJ
PACCMAD-BEP
+
the clade
I i
-
:!-.( .,:..:
Centothecoideae, Mi-
loideae,
DOGMA
from
lences extracted
multitaxon
fasta files
)
MUSCLE
gene sequences using -.:::'
lign
-i
..
.
, '
van der 1979; Regal, 1982; Cox, 1991; Linder,
Pijl,
:
1998; Weller 1998; Givnish 1999; Cully
et al., et al.,
To
ii evaluate
,11
)08).
in
'
Clark
et al.. I9«;
son 2007a, Bouche-
et al., b; tests of correlate*
drained or (In
)
,,!(!
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I ii i
Iclirr
: - ' :
|( i: I' >, :
.
(1985), Givnish (1999, 2000, 2004, 2007),
el al.
<,::
IDMH..;. oil
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:
ingroups
as
iied
ii
I
;
&
models Meade, 2006
(Pagel
u\
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i
iii
. I! ,
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II.,
il . , ^ . . . -Till hi"!'
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',v,
i : i
ii
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&
Moore
al, 2007; al, 2007; Whitfield
et et
I I 'i
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'-:.(
,
" ML
: ' H
.11,1111
I >' all laxa in the tree (see
2000.
al,
et
>
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I'
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ll Hill i,i
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(Appendix
es within those families
2).
V' 111 III V, 1 lh.
nV
plants via
Henderson
(1971, 1979), (1986), Stiitzel (1986, 1990),
ListabarthllO"!
,.
ihere were 25,107
-ps (Fig. ()\erall,
2).
:
,..,... ,.i
;-i
:,i
Appendix
et (2009)
al. (sec;
8
MP
Hordeum
plastome phylogeny
graminids
Triticum
Agrostis
=
Length 152,366 steps Bambusa
Oryza
=
CI 0.384, CI' 0.31 WrSaccharum
Mf
Poaceae
Sorghum
83 taxa (68 monocots)
100 100 Zea
Eieusine
109,1 34 aligned bases
100
Pueiia
Anomochioa
25,107 informative characters
94
—
Streptochaeta
Ecde'tocoiea
100 100 "|
Ecdeiocoleaceae
{ GeorgeanthaA
n
Joinvillea piicata
100|
—
Joinvilleaceae
ascendens
Joinviflea
Fiageilaria Flagellariaceae
Poales
Thamnochortus
100 Restionaceae
restiids
i
Centrofep/s Centrolepidaceae
Mayaca
Mayacaceae
xyrids {
byngonan
thus Eriocaulaceae
Abolbodo
Xyridaceae
Cyperus Cyperaceae
100 -
r
cyperids
Juncus Juncaceae
Thurnia Thurniaceae
Potarophytum Rapateaceae
Spargan/um
Typh
Typha ]
Neoregelia
Oft-
l
mv-Puya
Jr
Pttcairnia
00
1
Bromeliaceae
Fosterella
Novia
Brocchinia
—
Chamaedorea
81i
1»
fElaeis Arecaceae Arecales
Li
Ravenea
Belosynapsis
100
Commelinaceae Commelinales
~\ ]
Tradescantia
Musa
Mu5aceae
Zingiberales
Reneaimia J
Zingiberaceae
Dasypogon
Dasypogonaceae Dasypogonales
]
King/a ]
Hesperafoe
8&-
.M-
Yucca
M\-Hosta
m
loon
Chlorophytum
Asparagaceae
Albuca
Asparagus
Lomandra
Nolina
Asparagales
Agapanthus
Amaryllidaceae
52
Phormium
Xanthorrhoeaceae
Iris Iridaceae
Curcuiigo Hypoxidaceae
Neoasteiia Asteliaceae
100
Apostasia
00
1 j Orchidaceae
]
Phaiaenopsis
-
100 Dioscorea Dioscoreaceae Dioscorea es
I
Pandanus Pandanaceae - Pandanales
Hum
-
100 Li Liliaceae Liliales
Lemna
-
Araceae Alismatales
Acorus americanus
100
I — Acoraceae Acorales
A corns calam us ] ]
'
Anethum
Panax
Heiianthus
94
Coffea
Spinacia
Cucumis
Eudicots
Medicago
Populus
100
Buxus
Piatanus
Nandina
100
Calycanthus Laura es
I
Liriodendron Magnoliales
94
Drimys Canellales
Piper Piperales
lliicium Austrobaileyal
Nuphar Nymphaeales
Amboreiia Amborellales
1000 changes
I
100%
Mayaca Mayacace
bootstrap support; of
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< 1 1 i I I i
B. Sm., B. melanacra L. B.
I ,.
100% 94%
bootstrap sister (with
,
IW7.
iMi al. 2007) Low-nutrient
et
ACCTRAN.
However, infertile soils are more likely than
mfened
favor (Givnish. 1980). the
to
fir,-
2000, 2004, 2007), as do sedg
;i..|
I,
J
±
....
unit node, lminch lengths averaged 1734 170 'iv :.,„<.' '
I. ; i . '
± ±
(mean SD) steps for palms, 2112 103 for
±
7821 1102
ids,
Fh
running from ilka through the
1416 for graminids. Rates of plastid sequence
mux
<":'!
:.-
,
:
ML
produced
a single, fully resolved, well-
''
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trap support as being mono-
that the ancestral habitat
had
commelinids in the for both highly infertih
>"
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ML
the tree was generally higher than that for the from Bromeliaceae
Cyperaceae, and Juncaceae
e,
!/
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or< n
ly,t} 'Villi IK-;, in I. "I i" ;.. '' ...
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more
provided a :h strongly
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in. :.
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86%
sister to Dasypogonales with bootstra
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