2. Relationships within Populus
•
P. trichocarpa and P.
balsamifera are sister
species: balsam
poplars (section
Tacamahaca)
•
Closely related to the
cottonwoods (section
Aigeros).
•
Natural hybrids form
at contact zones
between species.
3. Relationships within Populus
•
•
•
The sister relationship of
P. balsamifera and P.
trichocarpa is supported
by most molecular data.
Levsen et al estimated a
very recent date of
divergence of ~75 Kya.
Recent molecular
phylogenies do not agree
on the relative placement
of the cottonwoods and
the balsam poplars.
P. balsamifera
P. trichocarpa
P. tremula
P. angustifolia
P. fremontii
adapted from Levsen et al 2012
4. POPCAN dataset
•
Genome BC’s POPCAN project is investigating the
genomics of Populus trichocarpa and P. balsamifera.
•
Main approach is to align short-read wholegenome shotgun sequences to reference genome
of P. trichocarpa.
•
•
•
Resequenced >300 samples of P. trichocarpa.
Resequenced >200 samples of P. balsamifera.
Resequenced many samples of other species of
Populus for phylogenetic context.
5. •
We can make a complete plastome phylogeny of the
North American cottonwoods and balsam poplars.
•
•
•
27 samples of P. trichocarpa
21 samples of P. balsamifera
Seven samples of other cottonwoods
8. Plastome alignment
• For most positions,
all reads agree on
the allele called.
• We used a
conservative
approach: infer
ambiguities and
low-coverage bases
as missing data.
9. Plastome alignment
• What about
ascertainment bias?
• Aligning to a
reference of an
ingroup species
could cause
artifacts.
10. • Alignment to different reference works as well!
• Slow-evolving plastome means that much of the
plastome is conserved across taxa.
11. • More missing data, but high coverage of genes.
• Populus alignment has 3% missing data.
• Manihot alignment has 44% missing data.
12. Salix eriocephala
Salix interior
Populus tomentosa
P. angustifolia GHE1
P. angustifolia Coal1
P. angustifolia AZBR107
P. deltoides Missou7Raju
P. deltoides Pdel181
Clade A
P. fremontii Pfre186
P. balsamifera ROS4
P. deltoides SO539SL
P. trichocarpa HALS30
Manihot
P. trichocarpa JASP30
P. trichocarpa PITS29
P. trichocarpa NASD8
P. trichocarpa STKG4
P. trichocarpa LAFY30
P. trichocarpa JEFF30
P. trichocarpa NPLN30
P. trichocarpa NECA14
P. trichocarpa TOBA23
P. trichocarpa NBON29
Clade T
P. trichocarpa CARS29
P. trichocarpa HAZH10
P. trichocarpa BULG11
P. trichocarpa ISKA6
P. trichocarpa SKNM10
P. trichocarpa KIMB16
Populus
Salix spp.
Populus tomentosa
P. balsamifera MIN11
P. balsamifera RNA13
P. balsamifera LAR15
P. balsamifera DEN5
P. balsamifera DUN13
P. balsamifera GIL7
P. balsamifera STO13
P. balsamifera KUU3
P. balsamifera MAN9
P. balsamifera FRE14
P. balsamifera CAR14
P. trichocarpa WLOW15
P. balsamifera SOU5
P. balsamifera EDM5
P. trichocarpa SHEL15
P. balsamifera FBK10
P. balsamifera FTM8
P. trichocarpa MCGR15
P. balsamifera AP5454
P. balsamifera POR1
P. balsamifera NWL2
P. balsamifera LAR6
P. balsamifera GRA10
P. angustifolia GHE1
P. angustifolia Coal1
P. angustifolia AZBR107
P. deltoides Pdel181
P. deltoides Missou7Raju
P. fremontii Pfre186
P. balsamifera ROS4
P. deltoides SO539SL
P. trichocarpa HALS30
P. trichocarpa JASP30
P. trichocarpa PITS29
P. trichocarpa STKG4
P. trichocarpa NASD8
P. trichocarpa NPLN30
P. trichocarpa Nisqually-1
P. trichocarpa NBON29
P. trichocarpa TOBA23
P. trichocarpa NECA14
P. trichocarpa CARS29
P. trichocarpa LONG29
P. trichocarpa JEFF30
P. trichocarpa LAFY30
P. trichocarpa QFRS16
P. trichocarpa ISKA6
P. trichocarpa MCHA19
P. trichocarpa HAZH10
P. trichocarpa BULG11
P. trichocarpa SKNM10
P. trichocarpa CHKD19
P. trichocarpa BELC18
P. trichocarpa KIMB16
P. trichocarpa ALAA20
P. trichocarpa LONG29
P. trichocarpa QFRS16
P. trichocarpa MCHA19
P. trichocarpa ALAA20
P. trichocarpa CHKD19
Clade B
P. trichocarpa BELC18
P. balsamifera MIN11
P. balsamifera RNA13
P. balsamifera LAR15
P. balsamifera GIL7
P. balsamifera DEN5
P. balsamifera DUN13
P. balsamifera STO13
Clade A
P. balsamifera MAN9
P. balsamifera FRE14
P. balsamifera KUU3
P. balsamifera SOU5
P. trichocarpa MCGR15
Clade B
P. balsamifera EDM5
P. balsamifera FBK10
Clade T
P. trichocarpa SHEL15
P. trichocarpa WLOW15
P. balsamifera CAR14
P. balsamifera FTM8
P. balsamifera AP5454
P. balsamifera POR1
P. balsamifera LAR6
P. balsamifera NWL2
P. balsamifera GRA10
•
Best ML trees from RAxML, bold lines indicate >95% bootstrap
support.
•
•
Rooted using Salix and an Old World Populus species.
Both alignments resolve the same topology.
13. •
P. trichocarpa and P.
balsamifera are in two
separate clades: clade B
and clade T.
•
Clade A contains the
cottonwoods: P.
deltoides, P. fremontii, P.
angustifolia.
•
Clades A, B, and T
diverged at
approximately the same
time.
14. •
Each clade is highly
supported.
•
Divergence between
clade B and clade T is
greater than divergence
within clade A, which
has multiple
cottonwood species.
15. •
Based on the Populus/Salix divergence date of 45 Mya:
•
•
Each of the three clades dates to 13-15 Mya.
The MRCA of the balsam poplars and cottonwoods is
~25 Mya.
16. •
These dates of plastome divergence are much older than
the estimated nuclear divergence between P. trichocarpa
and P. balsamifera.
•
How to explain this discrepancy?
18. Chloroplast capture
Salix eriocephala
•
•
•
Unlikely.
In this case, the
capturing species should
have one haplotype that
reflects the species it
captured from.
Both P. balsamifera and
P. trichocarpa have
significant sequence
variation within each
clade.
Populus tomentosa
P. balsamifera MIN11
P. balsamifera RNA13
P. balsamifera LAR15
P. balsamifera DEN5
P. balsamifera DUN13
P. balsamifera GIL7
P. balsamifera STO13
P. balsamifera KUU3
P. balsamifera MAN9
P. balsamifera FRE14
P. balsamifera CAR14
P. trichocarpa WLOW15
P. balsamifera SOU5
P. balsamifera EDM5
P. trichocarpa SHEL15
P. balsamifera FBK10
P. balsamifera FTM8
P. trichocarpa MCGR15
P. balsamifera AP5454
P. balsamifera POR1
P. balsamifera NWL2
P. balsamifera LAR6
P. balsamifera GRA10
P. angustifolia GHE1
P. angustifolia Coal1
P. angustifolia AZBR107
P. deltoides Pdel181
P. deltoides Missou7Raju
P. fremontii Pfre186
P. balsamifera ROS4
P. deltoides SO539SL
P. trichocarpa HALS30
P. trichocarpa JASP30
P. trichocarpa PITS29
P. trichocarpa STKG4
P. trichocarpa NASD8
P. trichocarpa NPLN30
P. trichocarpa Nisqually-1
P. trichocarpa NBON29
P. trichocarpa TOBA23
P. trichocarpa NECA14
P. trichocarpa CARS29
P. trichocarpa LONG29
P. trichocarpa JEFF30
P. trichocarpa LAFY30
P. trichocarpa QFRS16
P. trichocarpa ISKA6
P. trichocarpa MCHA19
P. trichocarpa HAZH10
P. trichocarpa BULG11
P. trichocarpa SKNM10
P. trichocarpa CHKD19
P. trichocarpa BELC18
P. trichocarpa KIMB16
P. trichocarpa ALAA20
Clade B
Clade A
Clade T
19. Incomplete lineage sorting
Salix eriocephala
•
•
•
Unlikely.
The two clades share
many nuclear alleles and
experience ongoing
gene flow.
Plastome data supports
this: several sampled
individuals show
mismatched plastome
haplotypes.
Populus tomentosa
P. balsamifera MIN11
P. balsamifera RNA13
P. balsamifera LAR15
P. balsamifera DEN5
P. balsamifera DUN13
P. balsamifera GIL7
P. balsamifera STO13
P. balsamifera KUU3
P. balsamifera MAN9
P. balsamifera FRE14
P. balsamifera CAR14
P. trichocarpa WLOW15
P. balsamifera SOU5
P. balsamifera EDM5
P. trichocarpa SHEL15
P. balsamifera FBK10
P. balsamifera FTM8
P. trichocarpa MCGR15
P. balsamifera AP5454
P. balsamifera POR1
P. balsamifera NWL2
P. balsamifera LAR6
P. balsamifera GRA10
P. angustifolia GHE1
P. angustifolia Coal1
P. angustifolia AZBR107
P. deltoides Pdel181
P. deltoides Missou7Raju
P. fremontii Pfre186
P. balsamifera ROS4
P. deltoides SO539SL
P. trichocarpa HALS30
P. trichocarpa JASP30
P. trichocarpa PITS29
P. trichocarpa STKG4
P. trichocarpa NASD8
P. trichocarpa NPLN30
P. trichocarpa Nisqually-1
P. trichocarpa NBON29
P. trichocarpa TOBA23
P. trichocarpa NECA14
P. trichocarpa CARS29
P. trichocarpa LONG29
P. trichocarpa JEFF30
P. trichocarpa LAFY30
P. trichocarpa QFRS16
P. trichocarpa ISKA6
P. trichocarpa MCHA19
P. trichocarpa HAZH10
P. trichocarpa BULG11
P. trichocarpa SKNM10
P. trichocarpa CHKD19
P. trichocarpa BELC18
P. trichocarpa KIMB16
P. trichocarpa ALAA20
Clade B
Clade A
Clade T
20. CA
2
1_
rp
o
C1
rp
cD
ac
C2
o
rp
2
rps I
atp
ps
ppsb E
pssbbF
bJL
H
atp
F
atp
rpl2
rps 0
rpl318
psa 3
ttr J
prenP
penW-UG
ttG -CCG
L
A
A
atp
U
-UC
trnR -UCC
trnG
U
S-GC
trnbI
ps K
psb -UUG
trnQ
clpP
petB
psbH
psbN
psbT
psbB
trnK-UUU
matK
SNPs on Populus trichocarpa reference plastome
Polymorphism within clade T
psbA
trnH-GUG
rps19
rpl2
rpl23
trnI-CAU
petD
Polymorphism within clade B
rpl14
rps8
rpl36
rps11
rpoA
Fixed polymorphism between T and B
rpl16
ycf1
5
trnL
-CA
A
nd
hB
ycf
2
rps
7
trn
rrn V-G
AC
16
trn
I-G
AU
trn
A-
s7
rp
23
C
UG
rrn
4.5 CG
rrnn5 -A UU
rrrnR -G
t N
trn
1
ycf
ndhA
5
rps1
ndhH
ndhD
ndhI
ndhG
ndhE
psaC
ccsA
trnL-UAG
ndhF
ycf1
3
trnN
-G
trnR UU
rrrn4 -ACG
r n5.5
rrn2
t
rnA
-UG
trn
C
I-G
AU
C
r
rn1
trn 6
VGA
hB
nd
AA
CA
Lt
trn f15
yc
SNP comparisons between
clades B and T show that some
genes are more variable than
others.
ycf2
AU
nI-C
trpl23
r
rpl2
9
rps12
rpl2
rps3
•
Selection acting on a gene or
genes in the plastome in one
lineage could lead to plastome
divergence.
pe
t
ce A
m
A
yc
ps f4
aI
•
_1
oC
rp
o
B
pe
trn tN
C-G
trnT
nE -G
trnY -U GU
U
trnD -GUA
-GU C
C
psb
M
psbD
ps aB
rps14
trnfM-CAU
trnG-UCC
psbZ
trnS-UG
A
psbC
psaA
ycf3
C
ndhhK
nd J
ndh
A
-GA
trnF -UAA
trnL
U
0UG
trnT4
rps
GA
trnS-G
cL
rb
B
atp E AU
C
atp M--UAC
trnnV
tr
Differential selection
21. CA
2
1_
rp
o
C1
rp
_1
oC
rp
o
B
pe
trn tN
C-G
trnT
nE -G
trnY -U GU
U
trnD -GUA
-GU C
C
psb
M
psbD
ps aB
rps14
trnfM-CAU
trnG-UCC
psbZ
trnS-UG
A
psbC
psaA
ycf3
C
ndhhK
nd J
ndh
A
-GA
trnF -UAA
trnL
U
0UG
trnT4
rps
GA
trnS-G
cL
rb
cD
ac
The most variable genes between
clades are psbA, rbcL, ycf1, and
rpoC.
pe
t
ce A
m
A
yc
ps f4
aI
C2
o
rp
2
rps I
atp
ps
ppsb E
pssbbF
bJL
H
atp
F
atp
rpl2
rps 0
rpl318
psa 3
ttr J
prenP
penW-UG
ttG -CCG
L
A
•
B
atp E AU
C
atp M--UAC
trnnV
tr
Differential selection
A
atp
U
-UC
trnR -UCC
trnG
U
S-GC
trnbI
ps K
psb -UUG
trnQ
clpP
Polymorphism within clade T
petD
Fixed polymorphism between T and B
rpl16
ycf2
AU
nI-C
trpl23
r
rpl2
9
rps12
rpl2
rps3
ycf1
5
trnL
-CA
A
nd
hB
ycf
2
rps
7
trn
rrn V-G
AC
16
trn
I-G
AU
trn
A-
s7
rp
23
C
UG
rrn
4.5 CG
rrnn5 -A UU
rrrnR -G
t N
trn
1
ycf
ndhA
5
rps1
ndhH
ndhD
ndhI
ndhG
ndhE
psaC
ccsA
trnL-UAG
ndhF
ycf1
3
trnN
-G
trnR UU
rrrn4 -ACG
r n5.5
rrn2
t
rnA
-UG
trn
C
I-G
AU
C
r
rn1
trn 6
VGA
hB
nd
AA
CA
Lt
trn f15
yc
Using branch-site tests of
selection, found significant
differential selection on ycf1 in
clade A, the Aigeros cottonwoods.
psbA
trnH-GUG
rps19
rpl2
rpl23
trnI-CAU
Polymorphism within clade B
rpl14
rps8
rpl36
rps11
rpoA
•
petB
psbH
psbN
psbT
psbB
•
No significant evidence of
selection between clades T and B.
trnK-UUU
matK
SNPs on Populus trichocarpa reference plastome
22. Conclusions
•
Plastome selection, while still not ruled out, is
not a complete explanation.
•
•
•
The Aigeros cottonwoods, as a group, may be
undergoing differential plastome selection.
If differential selection is acting on clades B
and T, evidence is not strong.
Still possible that selection may be acting on
the tightly linked mitochondrial genome.
23. Conclusions
•
Plastome phylogeny tells a detailed story of a
single facet of the history of these two species:
this story is obscured by more recent events in
the nuclear loci.
•
Population genetic studies confirm the sister
relationship of P. trichocarpa and P. balsamifera.
•
However, the cytonuclear discordance must be
capturing a real historical event that predates
the Pleistocene bottleneck.
24. Acknowledgements
• Cronk Lab collaborators:
• Charles Hefer, Armando Geraldes, Natalia
Kolosova
• POPCAN project PIs and funders:
• Carl Douglas, Shawn Mansfield
• University of British Columbia
• Genome BC
