1
Text S1 Identifying Genets After inspecting a plot of pairwise differences in genetic
2
distance among all samples (Fig S2) we determined that only those multilocus genotypes were
3
clonemates that shared identical alleles at all loci. Note that differences between clonemates can
4
arise when somatic mutations and/or genotyping error has introduced variation. Such variation
5
would likely be in the form of one single-step mutation at one of the alleles of the genotyped
6
loci. We did not collapse such multilocus genotypes into multilocus lineages (Arnaud-Haond et
7
al. 2007) because at least in the haploid S. ‘fitti’ mutations can be passed on to the next
8
generation and thus might be the target of selection. Further, we aimed to reduce the risk of
9
wrongly collapsing distinct genets into multilocus lineages. Genotypic diversity indices were
10
calculated with GENODIVE (Table S4, Meirmans & Van Tienderen 2004).
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
Text S2 Detecting Multiple Infections. Technical issues such as genotyping errors can lead to
different allele calls between runs (Table S5, FL4 1160). Even within loci, small alleles amplify
better then large alleles and these differential efficiencies might be exasperated in PCRs on coinfections due to the increased competition for resources. Further, there might be differences in
amplification efficiency across loci in double infections (Fig S2). Biological explanations
include that infecting strains indeed change over time, but while we sometimes observed
secondary infections in colonies in no case was there a loss of an infecting strain (Table S5). In
some instances genetic diversity might have been the result of somatic mutations, which we
inferred in cases were multilocus genotypes across time and space were nearly identical but
differed by just one single-step mutation at one of the loci (Table S5, Cu 1993, Fl4 1160). In
those colonies that harbored two clearly distinct S. ‘fitti’ strains (Table S5, Cu2 1988, Cu2 1990),
recombination between co-infecting strains appeared to break up original haplotypes indicating
that the coral host might provide S. ‘fitti’ strains the opportunity for close contact and thus sexual
reproduction. Similar observations have been made in trypanosomes that infect insects
(Akopyants et al. 2009; Jenni et al. 1986; MacLeod et al. 2005; Schmid-Hempel et al. 2011).
1
26
Supplemental Figures and Tables
27
Table S1 Microsatellite loci for Caribbean Symbiodinium ITS2 type A3 (S. ‘fitti’). Given are the locus name, fluorescent dye label, the
28
primer sequence, repeat motif, the annealing temperature for the polymerase chain reaction, and the Genbank Accession number. Tails
29
were added to some primers in which case the tail was fluorescently labeled instead of the forward primer. N alleles = number of
30
different alleles; h = diversity calculated as 1 – the sum of the squared population allele frequencies based on 670 samples. Tails (5’ –
31
3’): T1 = GGCTAGGAAAGGTTAGTGGC, T2 = TCATACATGTCTCTCAGCGTAAAC, and T3 =
32
ACCAACCTAGGAAACACAG, T4 = GACTATGGGCGTGAGTGCAT.
Locus
Dye
Primer (5’ – 3’)
Repeat
N
h
alleles
A3Sym_01*
VIC
F: AACATGACCTGAGAGAGTGGT
R: TTGCGCAAAGGCTTGCAGAATCAC
A3Sym_03*
6FAM
F: GTACCTGCTCCCATGGCGAT
(AG) 9..20
Temp
Tail
(°C)
Ascension
Number
8
0.763
55
T4
HM802880
(CGT) 8
4
0.556
56
T2
HM802881
(CTG) 8
4
0.547
56
T3
HM802882
(GAT) 9
5
0.465
56
T1
HM802883
(AAC) 4
4
0.070
55
NA
HM802884
(ACA) 5..11
2
0.499
60
NA
HM802885
bp..(AG) 11(AC) 8
R: ACATGTCGCCAAGATGCCTGACCA
A3Sym_07*
NED
F: CCTGCTAACTTTGTTGCGGTAGG
R: GCAGACGTCAAGAGCCACAGCT
A3Sym_09*
PET
F: TCAGATGCCAAGAGCCCAGAGT
R: CACTGTTTGGTAGGATGCGCTGAA
A3Sym_18*
HEX
F: CGATCACGACAACACCAGAAGC
R: TGAACTGAGCGATTACTGTCCAGG
A3Sym_27*
NED
F: AACACAGCTAAGATGCCTGCT
R: GTGTTTTTGTTGGTGGTGTTGTCG
bp..(AGC) 3
2
Locus
Dye
Primer (5’ – 3’)
Repeat
A3Sym_28*
PET
F: CGAGCCCGCCAAAGCTTCGAGGTT
(GAT) 6
5
0.391
52
NA
HM802887
(GGCAGC) 3
3
0.098
52
NA
HM802888
(AGTAGC)5
14
0.815
55
NA
HM802889
(CAC) 5
5
0.502
52
NA
HM802890
(TATG) 7
6
0.657
55
T3
KF787091
TAG(9)
6
0.681
55
T4
KF787092
TATC(6)
4
0.543
55
T2
KF787093
N
h
alleles
Temp
Tail
(°C)
Ascension
Number
R: TGACCCAGAGTTATCAGTGATCG
A3Sym_31*
HEX
F: GTGGTATAGTGTAGTGGCTGG
R: GACCGCATTCGACAGTTAGGCT
A3Sym_32*
6FAM
F: GGTCGCAGTGGCAGTGGCAGTA
(AGC) 4..10
bp..(CAG) 10
R: ACTGACTGCTGCGCACAAAGG
A3Sym_41*
6FAM
F: CACCACTACACTGAATGGCGAC
R: CGATGGCGATGCGATGGTGAT
A3Sym_02
NED
F: GCATAAACACGTTTTCTTCCAA
R: TTGCATACTTGCACTTGTGG
A3Sym_08
VIC
F: TGGTTTAGGGTTAGGGGTCA
R: GGGGGCCTCTACAAAAGAAA
A3Sym_48
6FAM
R: CCATCATGACCATCTGGCTA
R: CCGCAAAAAGTGTTACTCACC
33
34
* From Reference (Pinzón et al. 2011)
35
36
3
37
Table S2 Acropora palmata host and symbiont samples genotyped. Some of the reefs were
38
sampled in a spatially explicit, random fashion using circular plots to keep sampling effort
39
constant (Clonal Structure = yes). Circular plots sampled on the same reef are indicated by letter
40
suffixes of the Site Code (e.g Ba7a and Ba7b). Number of complete multilocus symbiont (NSf)
41
and host genotypes (NAp) are given.
Region
Bahamas
Site Code Reef Name
Ba1
Ba10
Ba11
Ba13
Ba15
Ba17
Ba18
Ba2
Ba3
Ba5
Ba7a
Ba7b
Ba8
Bahamas Total
Bonaire
Bo1a
Bo1b
Bonaire Total
Curacao
Cu1a
Cu1b
Cu1c
Cu2a
Cu2b
Cu3a
Cu3b
Cu5a
Cu7
Curacao Total
Dom Rep
Dr1
Dom Rep Total
Latitude Longitude Clonal
structure
Great Iguana
26.7075 -77.154
Yes
LSI
23.7691 -76.096
Little Ragged Island 22.1538 -75.687
Adelaine Cay
22.1734 -75.703
Elkorn Cay
22.3283 -75.783
Johnson Cay
22.3331 -75.779
Nairn Cay
22.352 -75.796
Halls Pond
24.3539 -76.57
Rocky Dundas
24.2788 -76.539
Bock Cay
23.8075 -76.16
Yes
Charlies Beach
23.7808 -76.104
Yes
Yes
Perry Shallow
23.7733 -76.095
Yes
5
Taylors Made
12.2238 -68.405
Yes
12.2234 -68.403
Yes
2
Blue Bay
12.1352 -68.99
Yes
12.1355 -68.99
Yes
BB1
12.1469 -68.987
Sea Aquarium
12.0838 -68.896
Yes
12.0831 -68.896
Yes
Puntu Oeste
12.0406 -68.783
Yes
12.0407 -68.783
Yes
SM1
12.2679 -69.128
Spanish Waters
12.0642 -68.853
6
Punta Cana
18.5275 -68.358
1
NSf
NAp
23
1
1
1
1
1
1
1
1
21
13
16
24
105
23
15
38
14
12
1
35
24
15
20
1
10
132
2
2
22
1
1
1
1
1
1
1
1
20
11
16
19
96
21
13
34
14
11
1
23
24
15
18
1
10
117
2
2
Region
Site Code Reef Name
Florida
Fl12b
Fl13d
Fl14a
Fl15a
Fl16b
Fl2
Fl4a
Fl4b
Fl5
Fl7a
Fl7b
Fl8
Fl9
Florida Total
Mexico
Me1
Me7
Mexico Total
Mona
Pr1
Pr3
Mona Total
Navassa
Na1
Na2
Na2b
Na3
Navassa Total
Panama
Pa1
Pa2
Pa3a
Pa3b
Pa4a
Pa7
Panama Total
Puerto Rico Pr10a
Pr11a
Pr6a
Pr7
Pr9a
Puerto Rico Total
Little Grecian
Horseshoe
Latitude Longitude Clonal
structure
25.1236 -80.297
25.1426 -80.258
25.0339 -80.349
25.0096 -80.375
25.2218 -80.211
24.456 -81.86
25.0179 -80.369
25.0179 -80.369
Yes
25.1184 -80.317
Yes
25.1395 -80.294
Yes
Boomerang Reef
Marker3
25.3525 -80.179
25.3733 -80.16
Chinchorro
Puerto Morelos
18.3833 -87.45
20.8306 -86.874
Key Largo
Elbow
French Reef
Molasses
CF
Rock Key
Sand Island
Yes
4
yes
1
Carmelita
Pajores
18.1032 -67.937
North Shelf
NW Point
NW P1
Lulu Bay
18.4135
18.4136
18.4139
18.3958
Bocas Del Drago
Wild Cayne
Bastimentos
9.41615 -82.331
9.3459 -82.172
9.265
-82.12
Tobobe
Bocas Del Toro
9.12268 -81.818
NA
NA
-75.023
-75.029
-75.03
-75.02
Yes
1
Yes
Yes
Yes
3
Tres Palmas 1
La Cordillera 1
Rincon
Aurora
Cayo Ron 1
18.3505
18.3797
18.2101
NA
18.1019
2
-67.267
-65.582
-67.159
-67.286
NSf
NAp
3
5
15
3
2
1
40
13
23
32
7
1
28
173
32
5
37
1
1
2
1
1
1
18
21
22
1
19
15
1
8
66
5
3
1
1
3
13
3
5
14
3
2
0
38
12
21
22
7
1
27
155
28
NA
1
1
2
1
1
1
18
21
21
1
19
14
NA
NA
55
5
3
1
1
3
13
Region
Site Code Reef Name
SVG
Sv1a
Sv3
Sv4
Sv5
Sv6
Sv7
Sv8
StVincent BC
Bequia
Canouan
Tobago Cays
Union Island
Mayreaux Gardens
Blue Lagoon
Sj2
Vi1
Vi2a
Vi2b
Vi2c
Vi4
Vi5
YP
Johnson’s Reef
Hawksnest Bay
SVG Total
USVI
Buck Island
Salt Pond
Latitude Longitude Clonal
structure
NA
13.015 -61.249
12.6943 -61.336
12.6253 -61.35
12.5916 -61.416
12.6322 -61.382
13.1285 -61.199
18.3358
18.3617
18.3472
18.3471
NA
18.2774
NA
USVI Total
Grand Total
-64.741
-64.774
-64.781
-64.781
Yes
Yes
Yes
-64.894
3
25
42
3
NSf
NAp
2
1
1
1
1
1
1
8
1
14
24
25
1
1
1
67
664
2
1
1
1
1
1
1
8
1
12
21
24
1
1
1
61
592
43
Table S3 Genotypic diversity of A. palmata and its symbiont S. ‘ftti’ in randomly sampled plots. N = sample size, Ng = Number of
44
Clones (equals expected genotypic diversity Ge), Go = observed genotypic diversity, Ndiv = corrected Nei’s diversity index
45
(Simpson’s), Neve = Evenness corresponding to Nei’s index, Ncsh = Corrected Shannon’s diversity index, Nush = Uncorrected
46
Shannon’s diversity index. All indices were calculated with Genodive, using a threshold of 0 and assuming a stepwise mutation
47
model. Only samples without missing data were included.
East/
Region
Pop
N
West
E
Bonaire
Mean
Ng
Go
Ndiv
Neve
Ncsh
Nush
Ng
Go
Ndiv
Neve
Ncsh
Nush
18
9
5.40
0.86
0.60
1.03
0.84
16
14.73
0.99
0.92
1.87
1.19
Bo1b
13
9
7.35
0.94
0.82
1.22
0.91
11
8.90
0.96
0.81
1.63
1.00
15.50
9.00
6.37
0.90
0.71
1.12
0.87
13.50
11.81
0.97
0.86
1.75
1.10
Cu1a
14
7
4.26
0.82
0.61
0.93
0.72
7
2.80
0.69
0.40
0.93
0.63
Cu1b
11
7
5.26
0.89
0.75
1.05
0.78
11
11.00
1.00
1.00
nan
1.04
Cu2a
10
6
3.33
0.78
0.56
0.97
0.65
7
5.56
0.91
0.79
1.12
0.80
Cu2b
23
4
1.44
0.32
0.36
0.38
0.28
10
3.75
0.77
0.38
1.00
0.78
Cu3a
15
7
6.08
0.90
0.87
0.92
0.81
12
9.78
0.96
0.82
1.53
1.04
Cu3b
18
7
5.79
0.88
0.83
0.88
0.80
11
8.53
0.94
0.78
1.22
0.99
15.17
6.33
4.36
0.76
0.66
0.85
0.67
9.67
6.90
0.88
0.69
1.16
0.88
Vi1
12
4
2.40
0.64
0.60
0.58
0.47
10
8.00
0.96
0.80
1.55
0.96
Vi2a
21
2
1.10
0.10
0.55
0.14
0.08
7
3.04
0.71
0.43
0.78
0.63
Vi2b
24
2
1.09
0.08
0.54
0.12
0.08
9
3.06
0.70
0.34
0.89
0.69
19.00
2.67
1.53
0.27
0.56
0.28
0.21
8.67
4.70
0.79
0.52
1.07
0.76
Mean
USVI
A. palmata
Bo1a
Mean
Curacao
S. ‘fitti’
1
East/
Region
Pop
N
West
W
Bahamas
A. palmata
Ng
Go
Ndiv
Neve
Ncsh
Nush
Ng
Go
Ndiv
Neve
Ncsh
Nush
Ba1
20
11
5.71
0.87
0.52
1.16
0.90
6
3.23
0.73
0.54
0.72
0.61
Ba5
20
2
1.72
0.44
0.86
0.27
0.27
8
3.92
0.78
0.49
0.90
0.74
Ba7a
11
1
1.00
0.00
1.00
0.00
0.00
3
1.46
0.35
0.49
0.41
0.26
Ba7b
16
3
1.47
0.34
0.49
0.33
0.26
6
4.92
0.85
0.82
0.80
0.73
Ba8
19
3
1.91
0.50
0.64
0.37
0.36
5
4.15
0.80
0.83
0.68
0.65
17.20
4.00
2.36
0.43
0.70
0.43
0.36
5.60
3.54
0.70
0.63
0.70
0.60
Fl4b
12
4
1.71
0.46
0.43
0.56
0.36
3
1.41
0.32
0.47
0.39
0.25
Fl5a
21
1
1.00
0.00
1.00
0.00
0.00
1
1.00
0.00
1.00
0.00
0.00
Fl7a
22
2
1.10
0.09
0.55
0.13
0.08
1
1.00
0.00
1.00
0.00
0.00
Fl9
20
1
1.00
0.00
1.00
0.00
0.00
1
1.00
0.00
1.00
0.00
0.00
18.75
2.00
1.20
0.14
0.74
0.17
0.11
1.50
1.10
0.08
0.87
0.10
0.06
Mean
Florida
S. ‘fitti’
Mean
Mexico
Me1
28
9
5.23
0.84
0.58
0.92
0.82
6
2.20
0.57
0.37
0.60
0.49
Navassa
Na3
18
4
2.19
0.58
0.55
0.51
0.43
18
18.00
1.00
1.00
nan
1.26
Panama
Pa1
20
2
1.60
0.40
0.80
0.25
0.24
8
2.99
0.70
0.37
0.87
0.67
Pa3a
19
1
1.00
0.00
1.00
0.00
0.00
5
1.78
0.46
0.36
0.55
0.40
Pa3b
14
4
1.85
0.50
0.46
0.52
0.39
9
7.54
0.93
0.84
1.16
0.92
17.67
2.33
1.48
0.30
0.75
0.25
0.21
7.33
4.10
0.70
0.52
0.86
0.66
Total
439
112
Mean
17.56
4.48
2.88
0.49
0.68
0.53
0.42
7.64
5.35
0.68
0.68
0.85
0.67
SD
4.62
3.00
2.05
0.34
0.20
0.41
0.33
4.30
4.46
0.32
0.25
0.51
0.36
Mean
191
2
48
Table S4 Population differentiation of S. ‘fitti’ across ten sites in the Caribbean using a dataset
49
that included all genotypes (n = 664) instead of only unique genets as in Table S4. Given are the
50
results of an AMOVA when considering all sites separately (a) and according to the East/West
51
Regions of the cnidarian host (b). Pairwise ΦPt values are shown in (c). All pairwise
52
comparisons were significant (p<0.05). Dom. Rep. (n = 2) and Mona (n = 2) were excluded. df =
53
degrees of freedom, SS = Sum of Squares, MS = Mean Sum of Squares, Est Var = estimated
54
variance, % = % of estimated variation. Φ = fixation index. ** P < 0.001.
55
Source
a)
Among Pop
Within Pop
Total
PhiPt
df
b)
Between Regions
Among Pop
Within Pop
Total
SS
MS
Est. Var.
%
Φ
9 913.561 101.507 1.615
650 1490.903 2.294
2.294
659 2404.464
3.909
41 0.41**
59
100
1 242.042 242.042
8 671.519 83.940
650 1490.903
2.294
659 2404.464
7 0.07**
36 0.39**
57 0.43**
100
0.295
1.447
2.294
4.036
56
57
c)
Puerto
Bonaire Curacao Rico
Bonaire
Curacao
Puerto
Rico
SVG
USVI
Bahamas
Florida
Mexico
Navassa
Panama
SVG
USVI
0.445
0.451
0.456
0.599
0.549
0.360
0.510
0.491
0.667
0.555
0.432
Bahamas
Florida Mexico
Navassa
0.246
0.343
0.522
0.461
0.537
0.511
0.633
0.568
0.389
0.112
0.283
0.292
0.354
0.339
0.421
0.325
0.232
0.370
0.421
0.401
0.382
0.610
0.507
0.301
58
59
3
0.229
0.566
0.452
0.468
0.496
0.459
0.484
0.643
0.498
0.382
60
Table S5 Within-colony diversity of Symbiodinium ‘fitti’. Given are haploid S. ‘fitti’ genotypes (in bp) for replicate samples (R) from
61
Acropora palmata colonies found on three reefs (Reef: Horseshoe - Fl7, Sand Island - Fl4, Sea Aquarium - Cu2) and sampled over
62
several years (Collection Date). Locus 18 was monomorphic in all samples and was omitted from the table. P = position of samples (B
63
= base of colony, T = growing tip of colony, U = underside of branch). * = same allele as initial sample, # = missing data.
Reef
R
Locus
Collection
1
2
27
28
3
31
32
41
48
7
8
9
Date
P
Interpretation
Fl4
1
212
175
196
226
186
212
251
135
179
177
129
138
07/29/03
1179
2
*
*
*
*
*
*
*
*
*
*
*
*
07/29/03
Cu2
1
210
171175
199
226
189
212
248251
#
179
174
129
138
03/11/10
1988
2
214
171
*
*
*
*
251
132
*
*
*
*
03/11/11
T
3
214
171
*
*
*
*
248251
132
*
*
*
*
03/11/11
T
4
214
171
*
*
*
*
251
132
*
*
*
*
03/11/11
T
5
214
171
*
*
*
*
251
132
*
*
*
*
03/11/11
B
6
210
175
*
*
*
*
248
135
*
*
#
*
03/11/11
U
Cu2
1
210
175
199
226
189
212
248
#
179
174
132
138
03/11/10
1990
2
210
*
199
223226
*
209212
248
132135
*
*
*
*
03/11/11
T
3
214
*
199
223226
*
209212
245
132135
*
*
*
*
03/11/11
T
4
210214
*
196199
223226
*
209212
245248
132135
*
*
*
*
03/11/11
T
5
210214
*
199
223226
*
209212
245248
135
*
*
*
*
03/11/11
U
6
210214
*
199
223226
*
209212
245248
132135
*
*
*
*
03/11/11
B
Cu2
1
214
171
199
226
186
215
251
#
179
174
129
135
03/11/10
1993
2
*
*
*
*
*
212215
*
132
*
*
*
*
03/11/11
T
secondary infection 1 yr later
3
*
*
*
*
*
215
*
132
*
*
*
*
03/11/11
T
or possible somatic mutation.
4
*
*
*
*
*
212215
*
132
*
*
*
*
03/11/11
T
Infections are present at
5
*
*
*
*
*
215
*
132
*
*
*
*
03/11/11
B
different ratios throughout
6
#
#
*
*
*
212
*
132
*
*
*
#
03/11/11
U
the colony.
1
Single infection
Double infection at initial
sampling maintained over 1
yr. Apparent sexual
recombination between
strains.
Single infection initially,
secondary infection 1 yr
later. Apparent sexual
recombination between
strains. Ratios differ.
Single infection initially,
Reef
R
Locus
Collection
1
2
27
28
3
31
32
41
48
7
8
9
Date
P
Interpretation
Cu2
1
216
171
199
226
186
215
251
132
179
174
129
135
09/26/02
T
3014
2
*
*
*
*
*
*
*
*
*
*
*
*
09/26/02
T
3
*
*
*
*
*
*
*
*
*
*
*
*
09/26/02
T
4
*
*
*
*
*
*
*
*
*
*
*
*
09/26/02
T
5
*
*
*
*
*
*
*
*
*
*
*
*
09/26/02
T
6
*
*
*
*
*
*
*
*
*
*
*
*
09/26/02
T
7
*
*
*
*
*
*
*
*
*
*
*
*
09/26/02
B
Fl4
1
214
179
196
226
186
212
#
135
183
177
129
138
06/17/09
6382
2
#
#
*
*
*
*
*
*
*
*
#
#
02/09/11
3
*
*
*
*
*
*
*
*
*
*
*
*
02/09/11
4
*
*
*
*
*
*
*
*
*
*
*
*
02/09/11
5
*
*
*
*
*
*
*
*
*
*
*
*
02/09/11
Fl4
1
214
179
196
226
186
212
251
135
183
177
129
138
06/17/09
6391
2
*
*
*
*
*
*
*
*
*
*
*
*
02/09/11
Single infection initially,
3
*
*
*
*
*
*
*
*
*
*
*
#
02/09/11
maintained 2 yr later
4
*
*
*
*
*
*
*
*
*
*
*
*
02/09/11
throughout the colony, some
5
*
*
*
*
*
*
*
*
*
*
*
*
02/09/11
missing data.
6
*
*
*
*
*
*
*
*
*
*
*
*
02/09/11
Fl4
1
214
179
196
226
186
212
251
135
183
177
129
138
09/28/09
6878
2
*
*
*
*
*
*
*
*
*
*
*
*
05/24/10
Fl4
1
214
179
196
226
186
212
251
135
183
177
129
138
09/28/09
Single infection throughout
6880
2
*
*
*
*
*
*
*
*
*
*
*
*
09/28/09
the colony.
2
Single infection throughout
the colony.
Single infection initially,
maintained 2 yr later
throughout the colony, some
missing data.
Single infection throughout
the colony, maintained over
1 yr.
Reef
R
Locus
Collection
1
2
27
28
3
31
32
41
48
7
8
9
Date
P
Interpretation
Fl7
1
214
179
196
226
186
212
251
135
183
177
129
138
08/04/10
2367
2
*
*
*
*
*
*
*
*
*
*
*
*
09/02/10
Single infection throughout
3
*
*
*
*
*
*
*
*
*
*
*
*
08/04/10
the colony, maintained over
4
*
*
*
*
*
*
*
*
*
*
*
*
08/04/10
1 yr.
5
*
*
*
*
*
*
*
*
*
*
*
*
01/20/11
Fl4
1
214
179
196
226
186
212
251
135
183
177
129
138
07/22/02
Single infection maintained
1079
2
*
*
*
*
*
*
*
*
*
*
*
*
07/29/03
over 1 yr.
Fl4
1
214
175
196
226
186
212
251
135
179
177
129
138
08/07/02
No change over one year but
1160
2
212
*
*
*
*
*
*
*
*
*
*
*
07/29/03
Fl7
1
210
179
196
226
186
212
248
135
183
177
129
138
09/02/10
Single infection maintained
1469
2
*
*
*
*
*
*
*
*
*
*
*
*
01/20/11
over 1 yr.
Fl7
1
210
179
196
226
186
212
248
135
183
174
129
138
09/02/10
Single infection maintained
1471
2
*
*
*
*
*
*
*
*
*
*
*
*
01/20/11
over 1 yr.
Fl7
1
214
179
196
226
186
212
251
135
183
177
129
138
09/02/10
Single infection maintained
1472
2
*
*
*
*
*
*
*
*
*
*
*
*
01/20/11
over 1 yr.
Fl7
1
210
179
196
226
#
212
248
135
183
177
129
138
09/02/10
Single infection maintained
1474
2
*
*
*
*
186
*
*
*
*
*
*
*
01/20/11
over 1 yr.
Fl7
1
210
179
196
226
186
212
248
135
183
177
129
138
09/02/10
Single infection maintained
1475
2
*
*
*
*
*
*
*
*
*
*
*
*
01/20/11
over 1 yr.
Fl7
1
216
175
196
226
186
212
257
135
183
177
129
138
09/02/10
Single infection maintained
1476
2
*
*
*
*
*
*
*
*
*
*
*
*
01/20/11
over 1 yr.
Fl7
1
#
179
196
226
186
212
248
135
183
174
129
138
09/02/10
Single infection maintained
1477
2
210
*
*
*
*
*
*
*
*
*
*
*
01/20/11
over 1 yr.
Fl7
1
214
179
196
226
186
212
251
135
183
177
129
138
08/04/10
Single infection maintained
2364
2
*
*
*
*
*
*
*
*
*
*
*
*
01/20/11
over 1 yr.
3
possible genotyping error or
somatic mutation at primer 1
Reef
R
Locus
Collection
1
2
27
28
3
31
32
41
48
7
8
9
Date
P
Interpretation
Fl7
1
214
179
196
226
186
212
251
135
183
177
129
138
09/28/09
Single infection maintained
6868
2
*
*
*
*
*
*
*
*
*
*
*
*
05/24/10
over 1 yr.
Fl4
1
212
175
196
223226
186
212
251
135
177
129
138
09/17/09
6887
2
*
*
*
*
*
*
*
*
*
*
*
05/24/10
1791
83
*
4
Double infection maintained
over 1 yr or single infection
with somatic mutations at
two loci.
64
65
66
67
68
69
70
71
72
Fig S1 Pairwise genetic distances among (A) Symbiodinium ‘fitti’ and (B) Acropora palmata
multilocus genotypes (MLGs, Table S2). There was a clear separation between the genetic
distances of ramets from the same genet (i.e. clonemates, bin 1) and genetic distances among
genets (> bin 1). The distribution of genetic distances indicates that like the host, Symbiodinium
‘fitti’ populations are undergoing sexual recombination. The host is diploid and each locus
contains many more allelic variants over a larger size range than the symbiont loci, which
explains the larger mean pairwise genetic distances among A. palmata MLGs.
5
73
74
75
76
77
78
79
80
81
82
83
84
85
Fig S2 Summary of the relative sensitivity for detecting the presence of additional S. ‘fitti’
genotypes within a sample. Co-infections were tested for eleven loci (1, 3, 7, 8, 9, 18, 27, 28, 31,
32, and 48). Total DNA from colonies harboring two genetically distinct S. ‘fitti’ strains was
mixed in varying proportions (95.0 to 5.0%). Most alleles diagnostic of a co-occurring strain
were detected when present in the population at 25%, or greater. Loci 18, 31 and 41 detected the
low abundance background strain if it had the larger allele but not the smaller allele (repeat units
between strains at each microsatellite locus differed from 1 to 6 repeat units) even at 5%
contribution of the background strain to total DNA. Locus 28 detected the background strain if it
had the smaller allele but not the larger allele at 5% contribution. Samples were conservatively
scored as containing multiple S. ‘fitti’ strains, if more than one allele was observed at just one
locus. Hence, the sensitivity of a genotyping assay to detect co-infections often reached 5% DNA
contribution from the less common strain.
86
87
88
89
6
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
Supplemental References
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Development of Leishmania in the Sand Fly Vector. Science 324, 265-268.
Arnaud-Haond S, Duarte CM, Alberto F, Serrao EA (2007) Standardizing methods to address clonality in
population studies. Molecular Ecology 16, 5115-5139.
Jenni L, Marti S, Schweizer J, et al. (1986) Hybrid formation between African trypanosomes during
cyclical transmission. Nature 322, 173-175.
MacLeod A, Tweedie A, McLellan S, et al. (2005) Allelic segregation and independent assortment in T.
brucei crosses: Proof that the genetic system is Mendelian and involves meiosis. Molecular and
Biochemical Parasitology 143, 12-19.
Meirmans PG, Van Tienderen PH (2004) GENOTYPE and GENODIVE: two programs for the analysis of
genetic diversity of asexual organisms. Molecular Ecology Notes 4, 792-794.
Pinzón J, Devlin-Durante M, Weber M, Baums I, LaJeunesse T (2011) Microsatellite loci for Symbiodinium
A3; (S. fitti) a common algal symbiont among Caribbean Acropora; (stony corals) and Indo-Pacific
giant clams (Tridacna). Conservation Genetics Resources 3, 45-47.
Schmid-Hempel R, Salathe R, Tognazzo M, Schmid-Hempel P (2011) Genetic exchange and emergence of
novel strains in directly transmitted trypanosomatids. Infection Genetics and Evolution 11, 564571.
108
109
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