Electronic Supplementary Material
Characteristics of clusters defined for clades A, B, and C
The Palys et al. (1997) 50% divergence rule is upheld for nearly all clusters in clades A and B that contain more than one “haplotype” (Table 1 of main text), suggesting that these clusters are ecologically distinct. The relationships depicted between “haplotypes” in the clade A ITS-2 networks (Figure 1a of main text) are further supported by their similarity to ITS-1 networks previously reported by Rodriguez-Lanetty (2003, Fig. 1a of main text). Most sequences common to both analyses (Symbiodinium linuchae, Symbiodinium pilosum, A3, A5 and AF333504) are placed in the same relative position within ITS-1 and ITS-2 networks. However, AF184948 and AF184949 could not be placed within the clade A ITS-2 network with 95% certainty, so a comparison of their relative position between the ITS-1 and ITS-2 networks is not possible. ITS-1 and ITS-2 networks cannot be compared for clades B, C and D, because they have few to no sequences in common. However, the same sequence (B1, Genbank accession AF333511) was designated as the root for both ITS-1 and ITS-2 clade B networks.
A broad range of divergence is particularly evident within Clade C, which contains an extremely large number of “haplotypes” that were connected in a single network by the statistical parsimony algorithm. This supports the hypothesis that lower divergences in clade C result from a recent speciation event (LaJeunesse 2005; Litaker et al. 2007) and likely contribute to the unresolved nature of published phylogenetic trees for this group. Due to the highly interconnected nature of this network, cluster membership is difficult to assign according to Palys et al. (1997). It is possible that the clade C network is actually one large cluster of minimally diverging sequences. Unfortunately, this hypothesis cannot be tested directly using the Palys et al. 50% rule, which requires the comparison of at least two hypothesized clusters that contain multiple “haplotypes”. However, given the high diversity of this clade and its wide distribution across two separate ocean basins (Indo-Pacific and Atlantic-Caribbean), clade C is unlikely to be monospecific (LaJeunesse 2005).Figure 2 (of main text) therefore depicts a rudimentary separation of the clade C haplotypes into 23 clusters of minimal sequence divergence using the Palys et al. (1997) method. When clade C ITS-2 sequences are analyzed using the cluster-based approach, generalists such as C1 and C3 are appropriately designated as the most ancestral haplotypes within two different species, with many rare haplotypes diverging from them. This configuration is typical of a dataset containing intraspecific data, and ameliorates the problem of “living ancestors” associated with traditional clade C phylogenies.
Ecological data for types A4 and A4a
Depth distributions are not significantly different for A4 and A4a, based on an unpaired t-test comparing all reported detections of these types (A4: N = 25; A4a: N = 32, from Table 1 below). This result was also generated when mixed symbiont assemblages were excluded (A4: N = 22; A4a: N = 30). Banaszak et al. (2006) investigated the mycosporine-like amino acids (MAAs) recovered from various Symbiodinium ITS-2 types (including A1, A3, A4 and A4a) and found that the clade A types examined produce 2 MAAs. Symbiodinium type A4a (collected from 2 Porites astreoides colonies and 1 Millepora alcicornis colony) produces the mycosporine-glycine type of mycosporine-like amino acid (MAA). This same MAA type was reported from symbionts (A4, A3, B1, and C1)within a Zoanthus sociatus colony. Two other colonies (Porites furcata) sampled by Banaszak et al. also contained Symbiodinium type A4, in addition to type B1. The symbionts of one of these colonies also produced the mycosporine-glycine type MAA only. Meanwhile, symbionts of the other colony produced 2 MAAs: 65.79% of the mycosporine-glycine type and 34.21% of the shinorine type. It is unclear whether the A4 type in this latter colony produced both MAAs or whether the shinorine type MAA was produced by Symbiodinium type B1; further sampling and study is required to resolve this and to determine whether MAA production is variable enough overall within Symbiodinium clade A to be an informative test of species designations. Warner et al. (2006) also included Symbiodinium ITS-2 types A4 and A4a in their investigations of symbiont photobiology. However, these two A types were not used in the same experiments and thus cannot be directly compared.
Agreement between the ‘types as species’ and cluster-based approach
The “types as species” and the cluster-based approach each view types B1 and B2 as members of distinct species. Traditional phylogenetic algorithms position types B1 and B2 within the B1 and B19 sub-clades respectively (Figure 6 in LaJeunesse 2005), however support is not reported for these positions. Meanwhile, types B1 and B2 were placed in the “B1”and “B9” clusters respectively (Figure 1b of main text), with 95% confidence. These clusters uphold the Palys et al. 50% rule in that the average pairwise variation within each cluster (“B1” = 2.12; “B9” = 2.32) is less than 50% of 5.03, the average pairwise divergence between the “B1”and “B9”clusters.Thornhill et al. (2008) found that type B2 is significantly more cold tolerant than B1, based on differential ability to recover photochemical efficiency after prolonged exposure to thermally depressed conditions. The cold tolerance of Symbiodinium B2 appears to influence its geographic distribution (Thornhill et al. 2008); this type is common in temperate western Atlantic habitats, but rarely detected in tropical and sub-tropical ecosystems. Previously, it has only been reported from northerly coral reef habitats, including the Florida Keys (LaJeunesse 2001; Santos et al. 2001) and Bermuda (Savage et al. 2002). Meanwhile, type B1 is commonly detected in tropical waters (Thornhill et al. 2008). Therefore, the available ecological data supports the distinction of B1 and B2 as separate species based on their relative differences in cold tolerance, which their geographic distributions appear to reflect.
Similarly, Sampayo et al. (2008) demonstrated that within the scleractinian host Stylophora pistillata, Symbiodinium ITS-2 types C8a and C78 exhibit higher thermotolerance than types C35a and C79 based on visual bleaching assessments, symbiont densities and estimates of photosynthetic efficiency. The “types as species” and cluster-based approaches each designate these four types as distinct species (Figure 2 of main text). However, the cluster-based approach provides additional information because connections between haplotypes in statistical parsimony networks are made with 95% certainty; therefore, the close proximity of the two bleaching sensitive types C35 and C79 in the statistical parsimony network is of interest due to the similar thermotolerances of these two types. In contrast, only the position of the C8 branch (which contains C8a) is statistically supported among the relationships generated using traditional phylogenetic algorithms (Figure 2 in LaJeunesse 2005).
Table 1. Meta-dataset of all Symbiodinium ITS-2 types reported from the Caribbean scleractinian coral, Porites astreoides. N = number of colonies sampled; BAR = Barbados; BEL = Carrie Bow Cay (Belize); FGB = Flower Garden Banks, Texas (U.S.A.); FK = Florida Keys (U.S.A.); LSI = Lee Stocking Island (Bahamas); MX = Puerto Morelos, Yucatan (Mexico); USVI = St. Croix, U.S. Virigin Islands;SB = severely bleached.
Citation / N / Ave. depth (m) / Types / Location / NotesSantos & LaJeunesse 2006 / 1 / 13.5 / A1.1, B1 / BAR / SB
1 / 14 / A4, B1, C3
3 / 27.5 / A14 / FGB
LaJeunesse 2002 / 1 / 2.5 / A3, A4a, B1 / MX
Santos & LaJeunesse 2006 / 4 / 1.5 / A4 / BAR
7 / 3 / A4 / SB (N = 2)
2 / 13.5 / A4 / SB (N = 1)
3 / 27.5 / A4 / FGB
Warner et al. 2006 / 4 / 2 / A4 / BEL
2 / 8 / A4
Santos & LaJeunesse 2006 / 2 / 13.5, 17.5 / A4, B1 / BAR
Banaszak et al. 2006 / 2 / 1, 7 / A4a / MX
LaJeunesse 2002 / 1 / 4 / A4a / LSI
Santos & LaJeunesse 2006 / 1 / 3 / A4a / BAR
3 / 13.5 / A4a
Thornhill et al. 2006 / 6 / 1.5 / A4a / FK
6 / 3 / A4a / LSI
Warner et al. 2006 / 8 / 8 / A4a / BEL
3 / 15 / A4a
Santos & LaJeunesse 2006 / 1 / 14 / A4a, B1, C3 / BAR
2 / 3, 13.5 / B1 / SB
2 / 13.5 / B1, C3
1 / 14 / B1, C3
1 / 13.5 / B1, C80 / SB
1 / 3 / C1
Warner et al. 2006 / 5 / 25 / C1a / BEL
Santos & LaJeunesse 2006 / 1 / 15 / C1a-i / USVI / green morph
Table 2. Summary of Symbiodinium rDNA sequences used for clusters-based analyses in this study including ITS-2type cf. LaJeunesse (2001, 2005), species description (if available) and GenBank accession number. The sequences were collapsed to haplotypes by the program TCS (version 1.21); these haplotypes are listed below and additionally represent the position of each sequence within the networks depicted in Figures 1 and 2 of this paper.
Clade / ITS-2 type / Species Description / GenBank Accession # / HaplotypeA / A1 / S. microadriaticum / AF333505 / S. microadriaticum (=A1)
A1 / A1 [1.1PM99] / EU449049 / S. microadriaticum (=A1)
A1 / A1 [C1med] / EU449048 / S. microadriaticum (=A1)
A1 / A1 [020073] / EU449031 / S. microadriaticum (=A1)
A1 / A1 [61] / EU449027 / S. microadriaticum (=A1)
AF180119 / S. microadriaticum (=A1)
S. microadriaticum subsp. condylactis (= S. cariborum) / AF333504 / S. microadriaticum subsp. condylactis
A1a /
A1a
/ EU449030 /A1a
A1med
/ EU449046 /A1med
A2 /S. pilosum
/ AF333506 / S. pilosum (=A2)A2 / A2 [169] / EU449044 / S. pilosum (=A2)
A2 / A2 [185] / EU449045 / S. pilosum (=A2)
[EPA4] / EU449026 / S. pilosum (=A2)
A3 / A3 / AF333507 /
A3
A3 / A3 [H80] / EU449047 / A3A3 / A3 [4.1PM99] / EU449051 / A3
A3 / A3 [328] / EU449034 / A3
A3 / A3 [7] / EU449037 / A3
A3 / A3 [350] / EU449039 / A3
A3a / A3a [TD1E] / EU449035 / A3a
A3b / A3b / EU449043 / A3b
A4 /
S. linuchae
/ AF333509 / S. linuchae (=A4)A4 / A4 [368] / EU449033 / S. linuchae (=A4)
A4 / A4 [34PM99] / EU449050 / S. linuchae (=A4)
A4a / A4a / AF499778 / A4a
A4a / A4a [45.1PM99] / EU449032 / A4a
A4a / A4a [Be182] / EU449040 / A4a
A4a / A4a [B10.802] / EU449052 / A4a
A5 / A5 [315] / AF333508 / A5
A6 / A6 / AY686646 / A6
A6 / A6 [ZAM96.10] / EU449042 / A6
A6 / A6 [TG3A] / EU449036 / A6
A7 / A7 [A3.302] / AY239360 / A7
A8 / A8 / AY258468 / A8
A8 / A8 [millte2a] / EU449038 / A8
A9 / A9 [STR1] / EU449028 / A9
A10 / A10 [LitRS] / EU449029 / A10
A11 / A11 [WS1] / EU449041 / A11
AF180120 / AF180120
AF184948 / AF184948
FREE / EU449053 / AF184948
AF184949 / AF184949
EU446104 / EU446104
EU446105 / EU446105
B / B1 /
S. pulchorum
/ AF333511 / S. pulchorum (=B1)B1 / B1 [B013a] / EU449092 /
S. pulchorum (=B1)
B12 / B12 [B01.12b] / EU449089 / S. pulchorum (=B1)B12 / B12 [B01.14] / EU449088 / S. pulchorum (=B1)
B14 /
B14 [B01.12a]
/ AY239362 / S. pulchorum (=B1)B14 / B14 [B02.60b] / EU449084 / S. pulchorum (=B1)
B14a / B14a [B02.60a] / EU449086 / S. pulchorum (=B1)
B1 / B1 [2culture] / EU449093 / S. pulchorum (=B1)
B1c / B1c [B01.3b] / EU449095 / S. pulchorum (=B1)
AF360550 / S. pulchorum (=B1)
AF360551 / S. pulchorum (=B1)
AF360554 / S. pulchorum (=B1)
AF360557 / S. pulchorum (=B1)
AF360558 / S. pulchorum (=B1)
AF360559 / S. pulchorum (=B1)
AF360562 / S. pulchorum (=B1)
AF360563 / S. pulchorum (=B1)
AF360565 / S. pulchorum (=B1)
AF360566 / S. pulchorum (=B1)
AF360568 / S. pulchorum (=B1)
AF360570 / S. pulchorum (=B1)
AF360572 / S. pulchorum (=B1)
AY876596 / S. pulchorum (=B1)
AY876597 / S. pulchorum (=B1)
AY876598 / S. pulchorum (=B1)
AY876599 / S. pulchorum (=B1)
AY876600 / S. pulchorum (=B1)
AY894809 / S. pulchorum (=B1)
AY894810 / S. pulchorum (=B1)
BE03.7 / EU449070 / S. pulchorum (=B1)
B1a / B1a [FL02.1] / AF499779 / B1a
B1a / B1a [PM99.59d] / EU449094 / B1a
B1b / B1b [Pm99.58b] / AF499780 / B1b
B1d / B1d [BE02.54a] / EU449096 / B1d
Isophylia
/ EU449064 / B1dB1e / B1e [BE02.50] / EU449097 / B1e
B1g / B1g [BE02.190b] / EU449098 / B1g
B1i / B1i [BE02.169b] / EU449099 / B1i
B2 / B2 [Med1] / AF333512 / B2
B2 / B2 [PorPlex] / AF333513 / B2
AF360564 / B2
AF360574 / B2
B2 / B2 [5culture] / EU449100 / B2
B3 / B3 [384culture] / AF333514 / B3
B4 /
S. muscatinei
/ AF333510 / S. muscatinei (=B4)B5 / B5 [PM99.40d] / AF499781 / B5
AF499782 / B5
B5a / B5a [Pm99.40a] / EU449101 / B5
BE03.16 / EU449068 / B5
culture571 / EU449066 / B5
B6 / B6 [Be02.103] / AF499783 / B6
B7 / B7 [Diekma.F2] / AF499784 / B7
AF458601 / B7
AF458602 / B7
AF458604 / B7
AF458605 / B7
AF458606 / B7
AF458607 / B7
AF458608 / B7
AF458609 / B7
AF458610 / B7
AF458611 / B7
AF458612 / B7
AF458613 / B7
AY894812 / B7
B7 / B7 [Pm99.223c] / EU449090 / B7
B8 / B8 [B99.2] / AF499785 / B8
AF360552 / B8
AF360553 / B8
AF360555 / B8
AF360556 / B8
AF360561 / B8
AF360567 / B8
AF360569 / B8
AF360571 / B8
AF360573 / B8
B9 / AF360560 / B9
B9 / B9 [B01.39] / AF499786 / B9
B19 / B19 [baker.B260] / EU449074 / B9
B19 / B19 [B02.2] / EU449073 / B9
B19 / B19 [579] / EU449075 / B9
B19 / B19 [B02.65] / EU449076 / B9
B19 / B19 [Be02.191] / EU449077 / B9
B19 / B19 [FL01.9] / DQ865212 / B9
B19a / B19a [B02.18] / EU449081 / B9
B22 / B22 [FL02.38] / EU449080 / B9
B02.71 / EU449078 / B9
stx77 / EU449067 / B9
B10 / B10 [FL301lg.Ma1] / AF499787 / B10
B11 / B11[FL02.75] / AY239361 / B11
B11 / B11[FL01.36] / DQ865211 / B11
B13 / B13 [B01.16b] / EU449091 / B13
B13a / B13a [B01.16a] / EU449085 / B13
AF458595 / B13
B15 / EF450626 / B15
B16 / B16 [baker.Sb31] / AY258469 / B16
B17 / B17 [baker.196071] / AY258470 / B17
B17 / B17 [BE02.147] / EU449083 / B17
B18 / B18 [FB4B] / AY258471 / B18
B18a / B18a [FB4A] / AY258472 / B18a
B20 / B20 [BE02.31] / EU449087 / B20
B21 / B21 [FL02.28] / DQ865213 / B21
BE03.39 / EU449071 / B21
BE03.390RI / EU449072 / B21
B23 / B23[B02.51] / EU449079 / B23
B24 / B24 [BE02.46a] / EU449082 / B24
AF360575 / AF360575
AF458596 / AF458596
AF458597 / AF458597
AF458598 / AF458598
AF458599 / AF458599
AF458600 / AF458600
AF458603 / AF458603
B02.74 / EU449069 / EU449069
culture 702 / EU449065 / EU449065
EU446106 / EU446106
C / C1 / S. goreaui / AF333515 /
C1
C1b / AY239363 / C1C1ca / EU449104 / C1
C1g / AY589730 / C1
C1n / EU449105 / C1
C72 / AY765407 / C1
C1c.C45 / EU449103 / C1c.C45
C4 / AF499794 / C1c.C45
C42 / AY765402 / C1c.C45
C1d / AY258488 / C1d
C1F / AY258490 / C1F
C1h / AY258473 / C1h
C1i / AY589731 / C1i
C1j / AY589732 / C1j
C1k / AY589733 / C1k
C1m / AY765398 / C1m
C3 / AF499789 / C3
C3b / AF499791 / C3
C3e / AF499793 / C3
C3g / AY589735 / C3
C3L / AY589738 / C3
C21.C3d / EU449102 / C3
C49 / AY589754 / C3
C3a / AF499790 / C3a
C3F / AY589734 / C3F
C3ha / AY589736 / C3ha
C3k / AY589737 / C3k
C3m / AY258497 / C3m
C3n / EU449106 / C3n
C5 / AF499795 / C5
C5b / AJ311942 / C5b
C6 / AF499796 / C6
C7 / AF499797 / C7
C12 / AF499801 / C7
C8 / AY239367 / C8
C8b / AY258475 / C8
C8a / AY239368 / C8a
C9 / AF499798 / C9
C10 / AF499799 / C10
C13 / AY589740 / C10
C10a / AY589739 / C10a
C11 / AF499800 / C11
C14 / AY589741 / C14
C43 / AY589749 / C14
C15 / AY239369 / C15
C2 / AF333518 / C15
C15F / AY589743 / C15
C55 / AY589759 / C15
C15a / AY258476 / C15a
C15c / AY258492 / C15c
C15d / AY258493 / C15d
C15e / AY589742 / C15e
C16 / AY258477 / C16
C16a / AY765399 / C16a
C17 / AY239370 / C17
C26a / EU449107 / C17
C18 / AY258478 / C18
C19 / AY258479 / C19
C20 / AY239371 / C20
C21 / AY239372 / C21
C21a / AY589744 / C21a
C58 / AY589762 / C21a
C22 / AY239373 / C22
C22a / AY239374 / C22a
C23 / AY239375 / C23
C24 / AY239376 / C24
C39 / AY258484 / C24
C41 / AY258486 / C24
C25 / AY239377 / C25
C26 / AY239378 / C26
C26a / AY258500 / C26
C27 / AY239379 / C27
C28 / AY239380 / C28
C29 / AY258494 / C29
C30 / AY589745 / C30
C31 / AY258496 / C31
C31a / AY589746 / C31
C31b / AY589767 / C31b
C32 / AY258498 / C32
C33 / AY765400 / C33
C34 / AY258499 / C34
C35 / AY765401 / C35
C35a / EU808002 / C35
C36 / AY258480 / C36
C37 / AY258481 / C37
C38 / AY258482 / C38
C38a / AY258483 / C38a
C40 / AY258485 / C40
C40b / AY589748 / C40
C40a / AY589747 / C40a
C42a / AY258487 / C42a
C42b / AY765403 / C42a
C44 / AY589750 / C44
C44a / AY589751 / C44a
C45a / AY765404 / C45a
C46 / EU449108 / C46
C46a / AY765405 / C46a
C47 / AY589752 / C47
C48 / AY589753 / C48
C50 / AY589755 / C50
C51 / AY589756 / C51
C52 / AY589757 / C52
C53a / EU449109 / C53a
C54a / AY765406 / C54a
C56 / AY589760 / C56
C56a / EU449110 / C56a
C57 / AY589761 / C57
C59 / AY589763 / C59
C60 / AY589764 / C60
C61 / AY589765 / C61
C62 / AY589766 / C62
C70 / AY589774 / C62
C64 / AY589768 / C64
C65 / AY589769 / C65
C65a / AY589770 / C65a
C66 / AY589771 / C66
C66a / EU449111 / C66
C66b / EU449112 / C66b
C67 / AY686647 / C67
C68 / AY589772 / C68
C69a / AY686648 / C69a
C71 / AY589775 / C71
C71a / AY589776 / C71a
C73 / AY765408 / C73
C74 / AY765409 / C74
C75 / AY765410 / C75
C76 / AY765411 / C76
C77 / AY765412 / C77
C78 / AY765413 / C78
C79 / AY765414 / C79
C90 / AJ621128 / C90
C91 / AJ621543 / C91
EU446111 / EU446111
EU446119 / EU446119
EU446120 / EU446120
EU446121 / EU446121
EU446122 / EU446122
EU446108 / EU446108
EU446110 / EU446110
EU446109 / EU446109
EU446114 / EU446114
EU446112 / EU446112
EU446115 / EU446115
EU446116 / EU446116
EU446117 / EU446117
EU446118 / EU446118
EU446113 / EU446113
D / D1 / D1 [MF1EPHY] / AF334660 /
D1
D1a_c / EU812739 /D1
D1a_e / EU812741 /D1
AP12 / EU449058 /D1
GF64 / EU449059 / D1Ha111b [D1] / EU449061 / D1
hidaka / EU449063 / D1
AF411415 /
D1
AF411416 /D1
D1a / D1a[EPA8] / AF499802 / D1aD1b / D1b [Ke219b] / EU449056 /
D1a
D2 / AY686649 / D1aAUSTD2 / EU449057 / D1a
D2
/ D2 [KE108] / EU449055 / D1aD4 / EU812744 / D1a
D4 / D4 [RS5] / DQ865214 / D1a
D5 / EU812743 / D1a
D5 / D5 [Platygyra_PG] / EU449054 / D1a
D5c / EU812746 / D1a
D7 / EU812747 / D1a
Ha111[D1b] / EU449060 / D1a
satospseudo / EU449062 / D1a
D1a_d / EU812740 / D1a_d
D1a_f/D6 / EU812742 / D1a_f/D6
D3 / D3 [A03.363] / AY686650 / D3
D5a / EU812745 / D5a
D8 / EU812748 / D8
EU446107 / EU446107
FJ377544 / FJ377544
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