ORIGINAL ARTICLE doi:10.1111/evo.12270 HOST-SPECIALIST LINEAGES DOMINATE THE ADAPTIVE RADIATION OF REEF CORAL ENDOSYMBIONTS Daniel J. Thornhill, 1 Allison M. Lewis, 2 Drew C. Wham, 2 and Todd C. LaJeunesse 2,3 1 Department of Conservation Science and Policy, Defenders of Wildlife, 1130 17th Street NW, Washington, DC 20007 2 Department of Biology, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802 3 E-mail: [email protected]Received April 8, 2013 Accepted September 4, 2013 Data Archived: Dryad doi: 10.5061/dryad.2247c Bursts in species diversification are well documented among animals and plants, yet few studies have assessed recent adaptive radiations of eukaryotic microbes. Consequently, we examined the radiation of the most ecologically dominant group of endosym- biotic dinoflagellates found in reef-building corals, Symbiodinium Clade C, using nuclear ribosomal (ITS2), chloroplast (psbA ncr ), and multilocus microsatellite genotyping. Through a hierarchical analysis of high-resolution genetic data, we assessed whether ecologically distinct Symbiodinium, differentiated by seemingly equivocal rDNA sequence differences, are independent species lin- eages. We also considered the role of host specificity in Symbiodinium speciation and the correspondence between endosymbiont diversification and Caribbean paleo-history. According to phylogenetic, biological, and ecological species concepts, Symbiodinium Clade C comprises many distinct species. Although regional factors contributed to population-genetic structuring of these lineages, Symbiodinium diversification was mainly driven by host specialization. By combining patterns of the endosymbiont’s host speci- ficity, water depth distribution, and phylogeography with paleo-historical signals of climate change, we inferred that present-day species diversity on Atlantic coral reefs stemmed mostly from a post-Miocene adaptive radiation. Host-generalist progenitors spread, specialized, and diversified during the ensuing epochs of prolonged global cooling and change in reef-faunal assemblages. Our evolutionary reconstruction thus suggests that Symbiodinium undergoes “boom and bust” phases in diversification and extinction during major climate shifts. KEY WORDS: Climate change, coral symbiosis, dinoflagellate, ecological specialization, phylogeography, speciation, Symbio- dinium. Adaptive radiations occur when lineages diversify in response to a variety of ecological opportunities (Gavrilets and Losos 2009; Glor 2010). These bursts of diversification occurred repeatedly at different taxonomic, spatial, and temporal scales throughout the history of life. Iconic examples of adaptive radiations include the Cambrian explosion (Valentine et al. 1999), the Cenozoic diversi- fication of therian mammals (Janis 1993; Agadjanian 2003), and more recent radiations of Darwin’s finches of the Gal´ apagos is- lands (Grant and Grant 2007), African cichlids (Seehausen 2006), Caribbean island Anolis lizards (Losos 2011), and Hawaiian sil- verswords (Baldwin et al. 1991). By comparison, relatively little is known about the adaptive radiations of microorganisms, including marine protists (see Falkowski et al. 2004). Their size, impover- ished geologic record, and difficulty in acquiring uncontaminated specimens for genetic analysis have limited our understanding of the tempo and mode of their diversification. Indications of the nature of adaptive radiations in eukary- otic microbes can be derived from the major groups of mod- ern eukaryotic phytoplankton—the dinoflagellates, diatoms, and coccolithophorids—following the mass extinction of marine life 352 C 2013 The Author(s). Evolution C 2013 The Society for the Study of Evolution. Evolution 68-2: 352–367
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ORIGINAL ARTICLE
doi:10.1111/evo.12270
HOST-SPECIALIST LINEAGES DOMINATETHE ADAPTIVE RADIATION OF REEF CORALENDOSYMBIONTSDaniel J. Thornhill,1 Allison M. Lewis,2 Drew C. Wham,2 and Todd C. LaJeunesse2,3
1Department of Conservation Science and Policy, Defenders of Wildlife, 1130 17th Street NW, Washington, DC 200072Department of Biology, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802
unesse and Thornhill 2011). When psbAncr data were compared
with ITS2 and multilocus microsatellite genotyping, concordant
patterns occurred across markers, indicative of species bound-
aries. Below we examine these results in the context of different
species concepts and consider abiotic and biotic factors poten-
tially underlying the diversification of Symbiodinium Clade C.
DELIMITING SPECIES LINEAGES WITH
HIGH-RESOLUTION GENETIC DATA
Although different species concepts emphasize different lines of
evidence, most share the idea that species are separately evolving
units (de Queiroz 2007; Hausdorf 2011). The phylogenetic species
concept, for example, identifies species using statistically signifi-
cant character differences resulting from evolutionary divergence
of populations over time (Donoghue 1985; de Queiroz 2007). Un-
der this concept, members of a species share more diagnostic ge-
netic or morphological characters with each other—and are hence
monophyletic—than with individuals from other species. Phylo-
genetic reconstructions based on the psbAncr revealed fine-scale
genetic diversity in Symbiodinium Clade C, including numerous
monophyletic clades that were differentiated from each other by
many nucleotide substitutions and indels. These phylogenetic pat-
terns are consistent with species-level distinctions, in that sister
lineages, as independently evolving metapopulations, appear to
have lost shared ancestral haplotypes (Wakeley 2008).
The frequent phylogenetic correspondence, or reciprocal
monophyly, of the independently sorting ITS (nuclear) and psbAncr
(chloroplast) provides strong support for the hypothesis that Clade
C comprises hundreds of species worldwide. Despite this, sev-
eral genetically and ecologically distinct psbAncr lineages shared
dominant ITS2 sequences (e.g., type C3). In such instances, the
unusual molecular evolution of the multicopy ribosomal array is
likely responsible for the discrepancy between markers. Evolu-
tion of rDNA begins as a mutation in one copy, which spreads
across copies via gene conversion or unequal crossing over, and
ultimately becomes numerically dominant within the genomes
of individuals undergoing genetic exchange in a population—
a process known as concerted evolution (i.e., Smith 1976;
Arnheim 1983; Dover 1986; Saito et al. 2002; Galluzzi et al.
2004). Concerted evolution exerts a stabilizing influence that can
prevent the spread of rare sequence variants, thereby maintaining
the numerically dominant rDNA sequence and masking lineage
divergence (Arnheim 1983; Dover 1986; Thornhill et al. 2007).
The shared C3 sequence that dominated the genomes of many
Symbiodinim Clade C lineages is likely a shared ancestral state, a
symplesiomorphy, which has not been replaced by a more derived
sequence.
Consequently, high-resolution genetic data indicate that
ITS2-nrDNA only approximates species richness within Clade
C. In cases such as Symbiodinium type C3 or type B1 from the
Caribbean, fine-scale genetic markers demonstrate that apparent
host-generalists actually consist of several specialized lineages
(Santos et al. 2004; Finney et al. 2010). As a result, populations
of other provisional host-generalists, including ITS2 types A1,
A3, C15, and D1a (D1–4), require reexamination with higher-
resolution genetic markers (see Pinzon et al. 2011; Wham et al.
2011). Future investigations may reveal that putative generalists
instead comprise several independent and ecologically specialized
species lineages, but others like S. goreaui may indeed associate
with many different host genera over a large geographic area, and
are thus true host-generalist symbionts (Fig. 3A).
The phylogenetic patterns of the psbAncr beg the questions:
do the discreet sequence clusters represent evolutionarily distinct
species? Or are they simply the accumulation of somatic muta-
tions through clonal evolution? Given the clonality of many in
hospite Symbiodinium populations (e.g., Thornhill et al. 2013),
clonal evolution and periodic selective sweeps (Palys et al. 1997)
might explain the concordant phylogenetic patterns of the chloro-
plast and nuclear loci. We therefore tested for evidence of ge-
netic recombination using multilocus population genetic data.
Three sympatric ITS2/psbAncr lineages were examined, includ-
ing C7 and C7a/C12 from the star corals, Orbicella spp., and
←−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−Figure 8. points for estimating timing of a most recent common ancestor (tmrca) between Pacific and Atlantic lineages. The Atlantic
Symbiodinium spp., examined by microsatellite analyses (Fig. 6) and associated with the reef corals Orbicella (C7 and C7a/C12) and
Siderastrea (C3Sid), are noted so as to delimit the ranges of interspecific versus interindividual sequence variation. Putative species
lineages are shaded according to their geographic origin (black = Indo-Pacific, brown = Atlantic). Stippled lines represent branches with
poor statistical support (Bayesian Inference). Red highlighting to the right of terminal branches indicates host-generalist lineages. (B)
Climate curve over the past 17 My based on oxygen-isotope measurements from deep-sea foraminifera (from Zachos et al. 2008). (C) Basic
estimation of the rate and tempo of lineage diversification in the chronogram (panel A). The gray shading in panels B and C encompasses
the time horizon of major climate shifts corresponding to the Miocene–Pliocene boundary.
3 6 2 EVOLUTION FEBRUARY 2014
ADAPTIVE RADIATION OF SYMBIOTIC DINOFLAGELLATES
C3Siderastrea from the massive starlet coral, Siderastrea siderea,
with 10 unlinked microsatellite loci. STRUCTURE analyses iden-
tified boundaries to sexual recombination between C7, C7a/C12,
and C3Siderastrea that corresponded to the symbionts’ phylogenetic
grouping and host affiliation (Fig. 6). Thus, host affiliation and
phylogenetic groupings superseded location as the primary fac-
tors in determining clustering. Furthermore, individuals belong-
ing to each ITS2/psbAncr lineage comprised recombinant (i.e.,
scrambled) allele combinations, indicating sexual recombination.
Members within each phylogenetic grouping, or lineage, appear
capable of engaging in sexual recombination, but are reproduc-
tively isolated from the constituencies of other lineages. These
three lineages therefore operate as distinct species according to
the biological species concept.
A common driver of monophyly, reproductive isolation, and
speciation is the selection of individuals with gene combinations
adapted to a resource or habitat (Ackerly et al. 2006; Losos 2009;
Glor 2010). Here, most psbAncr lineages contained individual hap-
lotypes recovered from only a single coral species or genus and
are thus functionally distinct species under the ecological species
concept. These clear ecological differences are consistent with the
adaption of many psbAncr clades to a particular host habitat, sug-
gesting the importance of distinct intracellular environments—
characteristic of different hosts—in the ecology and evolution of
these dinoflagellates. Indeed, host identity appears to be the pri-
mary ecological factor, or α-niche axis, of lineage diversification
in Symbiodinium (Figs. 3, 4, 6; LaJeunesse 2005; Ackerly et al.
2006; Finney et al. 2010; Glor 2010; LaJeunesse et al. 2010).
In addition to the Symbiodinium associated with hosts that verti-
cally transmit their symbionts, many host-specific lineages were
found associated with Caribbean Cnidaria that must horizontally
acquire symbionts from the environment at the start of each gen-
eration. This indicates that vertical transmission is unnecessary
for the evolution of host-specialized Symbiodinium spp. Further-
more, we found examples of hosts that harbored several phylo-
genetically independent and host-specific endosymbionts across
their range (e.g., Fig. S2), suggesting that endosymbionts evolved
along similar ecological axes in different locations (i.e., paral-
lel evolution) and that speciation through ecological selection is
a major recurrent theme throughout the evolutionary history of
these dinoflagellates.
Beyond host associations, many monophyletic and host-
specific psbAncr clades within the C3-group contained geograph-
ically segregated haplotypes (e.g., in symbionts of Orbicella,
Siderastrea, Agaricia), suggesting that spatial isolation acts as
a secondary or β-niche axis of divergence in Symbiodinium evo-
lution (Ackerly et al. 2006; Glor 2010). This spatial partitioning
mirrored the presence of distinct coral reef species assemblages
(Briggs 1974), as well as the genetic partitioning of several shal-
low water species in the Greater Caribbean (Fig. 1; Taylor and
Helberg 2003; Baums et al. 2005), that relate to theoretically
expected patterns of allopatry based on major surface currents
(Cowen et al. 2006) and long-standing environmental gradients
(Chollett Ordaz 2011). Moreover, these phylogeographic patterns
are consistent with previous findings of genetic structure in Sym-
biodinium populations at scales encompassing several hundred
kilometers, or less (e.g., Santos et al. 2003; Howells et al. 2009;
Thornhill et al. 2009; Andras et al. 2011). Limited connectivity
among Symbiodinium populations probably results from a combi-
nation of geographic barriers such as prevailing currents, limited
dispersal capacity of free-living cells, high local recruitment or
retention, or density-dependent barriers preventing long-distance
migrants from successfully penetrating habitats that are already
dominated by other Symbiodinium genotypes (reviewed in Thorn-
hill et al. 2009). Finally, different local and regional conditions
may also select for locally adapted genotypes (Chollett Ordaz
2011; Howells et al. 2012).
Taken together, these ecological, geographic, reproductive,
population genetic, and phylogenetic patterns suggest that Sym-
biodinium Clade C could consist of hundreds of species globally.
These findings also point to major biotic and abiotic factors—host
specialization and geographic isolation—shaping Symbiodinium
evolution. The following section considers these observations in
the context of the paleo-history of the Caribbean Basin in order
to make general inferences about their evolutionary history with
reef corals.
A SYNTHESIS OF THE INTERPLAY BETWEEN
PALEO-HISTORY, GEOGRAPHIC ISOLATION, AND
HOST SPECIALIZATION
Phylogenetic comparisons between Cnidaria and Symbiodinium
indicate a lack of co-speciation over tens of millions of years
(Rowan and Powers 1991; LaJeunesse 2005; Pochon et al. 2006;
this study). A more dynamic process of partner recombination
and coevolution must be at work to explain the existence of nu-
merous closely related endosymbionts associated with distantly
related hosts (LaJeunesse 2005). Evidence from our phylogeo-
graphic and molecular clock analyses (Figs. 4, 8) indicate that
an acceleration of lineage diversification occurred with the sep-
aration of the Atlantic from the Pacific during the late Miocene
and early Pliocene. Continental drift and tectonic uplift initiated
major changes in ocean circulation patterns that coincided with
the overall reduction in the planet’s temperature and atmospheric
CO2 concentration (Haug and Tiedemann 1998; Zachos et al.
2001, 2008; Pearson and Palmer 2000). Terrestrial changes dur-
ing this time included a drying of the climate, significant turnover
in terrestrial mammals, and expansion of C4 grasses (Haq et al.
1987; Ruddiman and Raymo 1988; Janis 1993; Cerling et al.
1997; Haug et al. 2001). In Caribbean marine environments, coral
species diversity initially increased with the complete closure of
EVOLUTION FEBRUARY 2014 3 6 3
DANIEL J. THORNHILL ET AL.
the Central American Seaway (Budd 2000). However, climate
shifts continued during the Plio–Pleistocene transition, notably
including the onset of northern hemisphere glaciation and asso-
ciated oscillations in temperature, pCO2, and eustasy, resulting
in continual ecological change (Zachos et al. 2001, 2008). These
effects were more pronounced in the Greater Caribbean, which ex-
perienced significant losses in coral diversity relative to the Pacific
(Budd 2000). Major changes in climate that induced reef faunal
turnover presumably affected Symbiodinium species assemblages
as well.
A once small number of species within Symbiodinium Clade
C, designated by ancestral ITS2 genotypes C3 and C1 that were
common to both ocean basins, served as the progenitors to the
radiation of the C1 and C3 groups. Presumably, these ancestors
or their descendants displaced Symbiodinium spp. that existed
before the changes in climate related to the Miocene–Pliocene
transition. According to the psbA data, a major burst in clado-
genesis began in the Atlantic during the late-Miocene (Fig. 8A).
By 3.1–4.6 Mya, genetic exchange between the Atlantic and Pa-
cific had ceased, resulting in independent evolutionary trajecto-
ries among Symbiodinium populations located in each ocean basin
(LaJeunesse 2005; LaJeunesse et al. 2010). The shifts in climate
conditions and the taxonomic composition of hosts that occurred
during and following this event ostensibly favored the diversi-
fication and specialization of Symbiodinium according to host
identity and geographic location, resulting in the diverse assem-
blage of endosymbiont species found on contemporary Caribbean
reefs (Figs. 4, 5, S1, S2). PsbAncr and ITS2 sequence data sug-
gest that Pacific lineages in the C3 group underwent a parallel
radiation during this time (LaJeunesse 2005); however, several
dominant host-generalist lineages remain in the Pacific C3 group
(Figs. 4, 8A).
There is precedent for the proliferation and shift in dom-
inance of other microbial groups during major environmental
change, perhaps as a result of adaptive innovation, reduced com-
petition, or extinctions that made available previously occupied
niches (Crouch et al. 2001; Falkowski et al. 2004). Surpris-
ingly, after the large number of extinctions associated the Plio-
Pleistocene transition, the Caribbean fauna of reef corals has re-
mained stable for approximately 1.5 My despite frequent, evenly
spaced oscillations in global temperatures (Jackson et al. 1996;
Jackson and Johnson 2000; Pandolfi and Jackson 2001). During
that period, reduced sea level and altered sea-surface currents
with each glacial cycle created oceanographic barriers to disper-
sal in the western Atlantic basin (Veron 1995) that hypothetically
provided opportunities for sequence coalescence and the evolu-
tion of numerous regionally localized psbAncr haplotypes (e.g.,
Figs. 5, S1, S2). Indeed, Pleistocene climates may have generated
regionally localized species radiations involving Symbiodinium in
Clades B (LaJeunesse 2005) and D (LaJeunesse et al. 2010).
Why was the C3 group of Clade C Symbiodinium more evo-
lutionarily successful in terms of the numbers of hosts and habitats
occupied in the Atlantic (and Pacific)? Although answers to this
question are speculative given the available data, some insight
may be gained by comparing the ecologies of extant species with
the historic climatic conditions during the radiation of this group
over the past 5 My. It is noteworthy that members of the C3 group,
usually occurred in colonies from deeper environments (>10 m),
where average temperatures and irradiance levels are lower and
less variable. By comparison, members of the C1 group occurred
in shallower habitats (∼5 m), where they would be subjected
to greater extremes in temperature and light conditions. Further-
more, type C1 examined in Australia is substantially more heat
tolerant than type C3 (referred to as type C2 in Berkelmans and
van Oppen 2006; Abrego et al. 2008; Jones et al. 2008; but see
Hume et al. 2013). This difference in diversity between the C1
and C3 groups in the Greater Caribbean is significant because
the Plio–Pliestocene was cold relative to the rest of the Ceno-
zoic (Fig. 8B; Weyl 1968; Burchardt 1978; Wolfe 1978; Haq
et al. 1987; Ruddiman and Raymo 1988). It is plausible, there-
fore, that a cool climate contributed to the diversification of the C3
group. Alternatively, fewer shallow water niches may have been
available to members of the C1 group in the Atlantic due to the
success of Symbiodinium Clade B (and to a lesser degree Clade
A) in animals from shallow Caribbean habitats (LaJeunesse 2002,
2005; Finney et al. 2010).
In summary, climate change, favoring the success of a few
ancestors that subsequently diversified principally through host
specialization in geographic isolation, likely drove the evolution
of Symbiodinium species diversity over the past 12 My. Under this
scenario, divergent selection, acting on genetic variation within
a population, favored adaptations that increased fitness in a par-
ticular habitat (Dieckmann and Doebeli 1999; Schluter 2001),
which is determined primarily by the intracellular host envi-
ronment. Disruptive selection likely opposed gene flow between
sympatric subpopulations adapting to different hosts. Genotypes
capable of associating with multiple host species (i.e., multiple
habitats) would be suboptimal because, under ecological the-
ory, these phenotypes experienced reduced fitness relative to a
specialist within any particular niche (Dieckmann and Doebeli
1999; Schluter 2001). Instead, reinforcement by disruptive se-
lection and assortative mating likely increased the prevalence of
genotypes that were competitively superior in symbioses with
a particular host taxon. This ongoing process would result in
reproductively isolated Symbiodinium populations, and eventu-
ally generate species assemblages partitioned mostly by host
identity (i.e., ecological speciation; Dieckmann and Doebeli 1999;
Schluter 2001, 2009).
Reef coral symbioses of the near future will encounter
a warmer climate and more acidic ocean than that of the
3 6 4 EVOLUTION FEBRUARY 2014
ADAPTIVE RADIATION OF SYMBIOTIC DINOFLAGELLATES
preceding 7 My (Burchardt 1978; Wolfe 1978; Ruddiman and
Raymo 1988; Pachauri and Reisinger 2007). Many Symbiodinium
spp. face displacement and extinction with increased sea-surface
temperatures and greater, or more erratic, seasonal fluctuations
in temperature that favor opportunistic species (LaJeunesse et al.
2009). Alternatively, some populations may acclimatize or adapt
to this environmental change or migrate with their host popula-
tions to more suitable locations. Although the specific outcomes
of these processes are uncertain, our reconstruction of evolution-
ary history suggests that Symbiodinium spp. respond to climate
change through “boom and bust” phases in diversification and
extinction. As with past changes in climate, the current warm-
ing may facilitate the rise and spread of host-generalists that are
competitively inferior under stable conditions but experience suc-
cess in a changing environment (e.g., Thornhill et al. 2006; Jones
et al. 2008; LaJeunesse et al. 2009).
ACKNOWLEDGMENTSThe authors sincerely thank K. K. Richter and K. M. Halanych for as-sistance with the phylogenetic analyses as well as J. Zachos for sharingthe most current adjusted oxygen-isotope data from deep-sea benthicforaminifera. The authors also thank E. Sampayo, A. Cecere, R. Smith,T. White, L. L. Walsh, H. Oxenford, and W. K. Fitt for contributing invarious ways to this work. This research was supported by the Pennsyl-vania State University, the IOC-UNESCO-World Bank targeted workinggroup on coral bleaching, and the National Science Foundation grants(IOB 544854 and OCE-09287664).
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Associate Editor: J. Wares
Supporting InformationAdditional Supporting Information may be found in the online version of this article at the publisher’s website:
Figure S1. Maximum Parsimony topology based on the psbAncr for haplotypes associated with Siderastrea siderea (ITS2
type C3).Figure S2. Maximum Parsimony topology based on the psbAncr for haplotypes associated with Agaricia and Leptoseris (ITS2 types C3, C3a, C3b, C3s,and C3q).Figure S3. Evanno’s Delta-K showing the change in likelihood between K = 3 and corresponds to populations designated by the two sister lineages (C7and C7a/C12) associated with Orbicella and the Symbiodinium C3 Siderastrea with Siderastrea siderea.Table S1. Symbiodinium samples, their ITS2 designations along with host species, depth of collection, and geographic origin.Table S2. Summary statistics on allele number and evenness among unique multilocus genotypes representing Symbiodinium lineages associated withOrbicella and Siderastrea from the Greater Caribbean of the western Atlantic.
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Supplemental for Siderastrea siderea associated Symbiodinium.−
PsbAncr haplotypes of Symbiodinium C3 associated with Siderastrea in the Greater Caribbean form a well-supported, monophyletic clade (Fig. S1). Phylogeographic patterns show that some populations are regionally localized. Within this clade there were various locally-endemic sub-clades and haplotypes, including lineages from the Bahamas, Barbados, Brazil and Curacao. A particular haplotype was only found in one sampling location. Figure S1, Maximum Parsimony topology based on the psbAncr for haplotypes associated with Siderastrea siderea (ITS2 type C3). The basal node of this tree connects to the topology presented in Fig. 4 (note «symbol at the node labeled C3 Siderastrea siderea in Fig. 4). Nodal support indicated as posterior probabilities (PP) above 0.85 next to the relevant node or asterisks for a PP = 1.00 (recovered from separate analyses using Mr. Bayes software, which produced a concordant tree topology). Colored symbols indicate the collection location of each haplotype corresponding to Fig. 1. The branch relating Brazil haplotypes with those of the Greater Caribbean is interrupted by slash marks to indicate that this lineage may be polyphyletic. Supplemental for Agaricidae associated Symbiodinium −
Multiple phylogenetically independent, or
paraphyletic, PsbAncr clades were found associated with Caribbean agaricidae: Agaricia and Leptoseris spp. (Figs. 4, S2). Many of these correlated with geography and corresponded to diagnostic intragenomic ITS2 sequence variants common in the genome. The two larger clades are abbreviated in Fig. 4 with a star symbol.
Samples designated as type C3b by ITS2 DGGE fingerprinting (data not shown) occurred at two positions in the phylogeny (designated by the superscripts 1 and 2) and represents the only case were ITS2 and psbA sequences did not correspond. This unusual finding was the only example of a polyphyletic ITS2 type in the psbAncr dataset and possibly resulted from homoplasy at the ITS2 level (or a highly unusual recombinant genotype). The C3b samples belonging to
2
separate groups could be differentiated according to minor differences in banding pattern upon close inspection of their ITS2-DGGE profiles (data not shown).
Figure S2 Legend, Maximum Parsimony topology based on based on the psbAncr for haplotypes associated with Agaricia and Leptoseris (ITS2 types C3, C3a, C3b, C3s, and C3q). Separate lineages insert at various locations in the phylogeny depicted in Figure 4 (note «symbol at the nodes in Fig. 4). Nodal support based on > 0.95 are indicated by asterisks. Colored symbols indicate the collection location of each haplotype corresponding to Fig. 1.
Supplemental Figure S3. Evanno’s Delta K showing the change in likelihood between between K=3 and corresponds to populations designated by the two sister lineages (C7 and C7a/C12) associated with Orbicella and the Symbiodinium C3Siderastrea with Siderastrea siderea.
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Table S1. Symbiodinium samples, their ITS2 designations along with host species, depth of collection, and geographic origin. GenBank accession numbers for psbAncr sequences are provides and were used to reconstruct the phylogenies in Figures 3–5, S1-S2. Shallow, intermediate and deep refers to collection depths ranging from 1-5, 6-10, and > 10 meters, respectively.
Sample I.D ITS-DGGE type
psbAncr Genbank accession number
Host Genus Host Species Region Location Site Collection Depth
27B_mexico_Montastraea_C7 C7 KF572268 Orbicella Orbicella faveolata Caribbean Mexico Puerto Morelos Shallow 30B_mexico_Montastraea_C7 C7 KF572248 Orbicella Orbicella faveolata Caribbean Mexico Puerto Morelos Shallow A02_10_Acropora_C3 C3 JQ043639 Acropora Acropora cerealis West Pacific GBR Heron Island Shallow A02_105_Platygyra_C3 C3 JQ043635 Platygrya Platygra daedalea West Pacific GBR Heron Island Shallow A02_12_Acropora_C3 C3 JQ043634 Acropora Acropora clathroata West Pacific GBR Heron Island Shallow A02_136_Coralimorph_C1 C1 KF572204 Coralimorpharia Coralimorpharia sp. West Pacific GBR Heron Island Intermediate A02_20_Acropora_C3 C3 JQ043640 Acropora Acropora gemmifera West Pacific GBR Heron Island Intermediate A02_27_Acropora_C3 C3 JQ043641 Acropora Acropora microclados West Pacific GBR Heron Island Shallow A02_30_Acropora_C3 C3 JQ043642 Acropora Acropora nasuta West Pacific GBR Heron Island Shallow A02_34_Acropora_C3 C3 JQ043643 Acropora Acropora palifera West Pacific GBR Heron Island Shallow A02_36_Acropora_C3 C3 KF572372 Acropora Acropora polystoma West Pacific GBR Heron Island Shallow A02_44_Acropora_C3 C3 JQ043644 Acropora Acropora tenuis West Pacific GBR Heron Island Shallow A02_47_Astreopora_C1 C1 KF572203 Astreopora Astreopora myriophthalana West Pacific GBR Heron Island Shallow A02_63_Favia_C3 C3 JQ043636 Favia Favia stellegera West Pacific GBR Heron Island Shallow A02_64_Favia_C3 C3 JQ043637 Favia Favia abdita West Pacific GBR Heron Island Shallow A02_70_Fungia_C1 C1 KF572205 Fungia Fungia sp. West Pacific GBR Heron Island Shallow A02_71_Galaxea_C1 C1 KF572195 Galaxea Galaxea fascicularis West Pacific GBR Heron Island Shallow A02_74_Goniastrea_C3 C3 JQ043638 Goniastrea Goniastrea aspera West Pacific GBR Heron Island Shallow A03_11A_Turbinaria_C3h C3h JQ043628 Turbinaria Turbinaria frondens West Pacific GBR Feather Reef North Deep A03_127_Symphyllia_C40 C40 KF572360 Symphyllia Symphyllia radians West Pacific GBR Feather Reef North Shallow A03_138_Coscinarea_C1 C1 KF572190 Coscinarea Coscinarea columna West Pacific GBR Feather Reef North Shallow A03_198_Tridacna_C1 C1 KF572172 Tridacna Tridacna maxima West Pacific GBR Rib reef south Shallow A03_2_Pachyseris_C3h C3h KF572373 Pachyseris Pachyseris speciosa West Pacific GBR Feather Reef North Deep A03_221_Podabacia_C3h C3h JQ043630 Podabacia Podabacia crustacea West Pacific GBR Rib Reef North Deep A03_238_Acropora_C3K C3K JQ043648 Acropora Acropora nobilis West Pacific GBR Rib Reef North Shallow A03_326_Turbinaria_C40 C40 KF572357 Turbinaria Turbinaria frondens West Pacific GBR Rib Reef South Intermediate A03_331_Turbinaria_C40 C40 KF572361 Turbinaria Turbinaria reniformis West Pacific GBR Rib Reef South Intermediate A03_333_Turbinaria_C40 C40 KF572358 Turbinaria Turbinaria frondens West Pacific GBR Rib Reef South Intermediate A03_337_Turbinaria_C40 C40 KF572359 Turbinaria Turbinaria reniformis West Pacific GBR Rib Reef South Intermediate A03_379_Echinopora C3 KF572363 Echinopora Echinopora lamellosa West Pacific GBR Curacao Island Intermediate A03_44_Pectinia_C3h C3h JQ043631 Pectinia Pectinia paeonia West Pacific GBR Feather Reef North Deep A03_50_Acropora_C1 C1 KF572189 Acropora Acropora tenuis West Pacific GBR Feather Reef North Deep A03_52_Leptoseris_C3h C3h JQ043627 Leptoseris Leptoseris yabei West Pacific GBR Feather Reef North Deep A03_56_Corallomorpharia_C1 C1 KF572173 Discosoma Discosoma rhodostoma West Pacific GBR Feather Reef North Deep
2
A03_6_Fungia_C3h C3h JQ043629 Fungia Fungia sp. West Pacific GBR Feather Reef North Deep A03_64_Fungia_C3h C3h KF572374 Fungia Fungia granulosa (?) West Pacific GBR Feather Reef North Deep A03_71_Pavona_C3h C3h JQ043630 Podabacia Podabacia crustacea West Pacific GBR Rib Reef North Deep A03_81_Acropora_C3K C3K JQ043645 Acropora Acropora humilis West Pacific GBR Feather Reef North Shallow A03_82_Acropora_C3K C3K JQ043646 Acropora Acropora nasuta West Pacific GBR Feather Reef North Shallow A03_83_Acropora_C3K C3K JQ043647 Acropora Acropora florida West Pacific GBR Feather Reef North Shallow A03_98_Galaxea C1 KF572194 Galaxea Galaxea fascicularis West Pacific GBR Feather Reef North Shallow ABA06_26_Siderastrea_C3 C3 KF572331 Siderastrea Siderastrea siderea Caribbean Bahamas Guana Cay, Abaco Shallow ABA06_28_Siderastrea_C3 C3 KF572332 Siderastrea Siderastrea siderea Caribbean Bahamas Guana Cay, Abaco Shallow B701_NNP1_Siderastrea_C3 C3 KF572319 Siderastrea Siderastrea siderea Caribbean Bahamas Lee Stocking Shallow B704_NNP4_Siderastrea_C3 C3 KF572318 Siderastrea Siderastrea siderea Caribbean Bahamas Lee Stocking Shallow B705_NNP5_Siderastrea_C3 C3 KF572317 Siderastrea Siderastrea siderea Caribbean Bahamas Lee Stocking Shallow Bah_428_M_faveolata_C12 C12 KF572239 Orbicella Orbicella faveolata Caribbean Bahamas Lee Stocking Deep Bah_441_M_franksi_C12 C12 KF572238 Orbicella Orbicella franksi Caribbean Bahamas Lee Stocking Deep Bah_442_M_franksi_C12 B1, C12 KF572240 Orbicella Orbicella franksi Caribbean Bahamas Lee Stocking Deep Bah_725_Montastraea_C12 C12 KF572237 Orbicella Orbicella franksi Caribbean Bahamas Lee Stocking Deep Bah01_10_Agaricia_C3 C3 KF572378 Agaricia Agaricia tenuifolia Caribbean Bahamas Lee Stocking Shallow Bah01_08_Agaricia_C3b C3b KF572385 Agaricia Agaricia agaricites Caribbean Bahamas Lee Stocking Shallow Bah02_10_C3_Leptoseris_C3 C3 KF572292 Leptoseris Leptoseries cuculata Caribbean Bahamas Lee Stocking Deep Bah02_43_C3_Leptoseris_C3 C3 KF572294 Leptoseris Leptoseries cuculata Caribbean Bahamas Lee Stocking Deep Bah02_44_C3_Leptoseris_C3 C3 KF572295 Leptoseris Leptoseries cuculata Caribbean Bahamas Lee Stocking Deep Bah02_62_Agaricia_C3 C3 KF572379 Agaricia Agaricia tenuifolia Caribbean Bahamas Lee Stocking Shallow Bah02_77_Siderastrea_C3 C3 KF572301 Siderastrea Siderastrea siderea Caribbean Bahamas Lee Stocking Shallow Baja04_124_Porites_panamensis C1 KF572208 Porites Porites panamensis Eastern Pacific Gulf of California La Paz Shallow Baja04_135_Psammocora_C1bf C1b-f KF572213 Psammocora Psammocora profundacella Eastern Pacific Gulf of California La Paz Intermediate Baja04_14_Porites_panamensis C1 KF572210 Porites Porites panamensis Eastern Pacific Gulf of California La Paz Shallow Baja04_143_Psammocora_C1bf C1b-f KF572214 Psammocora Psammocora superficialis Eastern Pacific Gulf of California La Paz Intermediate Baja04_30_Porites_panamensis C1 KF572209 Porites Porites panamensis Eastern Pacific Gulf of California La Paz Shallow Baja04_34_Porites_panamensis C1 KF572207 Porites Porites panamensis Eastern Pacific Gulf of California La Paz Shallow Bar05_100_Diploria_C3 C3 KF572356 Diploria Diploria strigosa Caribbean Barbados Atlantis Bank Reef Deep Bar05_102_Erythropodium_C3 C3 KF572288 Erythropodium Erythropodium caribaeorum Caribbean Barbados Atlantis Bank Reef Deep Bar05_104_Montastraea_C7a C7a KF572222 Orbicella Orbicella faveolata Caribbean Barbados Atlantis Bank Reef Deep Bar05_113_Agaricia_C3 C3 KF572413 Agaricia Agaricia lamarcki Caribbean Barbados Atlantis Bank Reef Deep Bar05_114_Leptoseris C3 KF572293 Leptoseris Leptoseris cucullata Caribbean Barbados Atlantis Bank Reef Deep Bar05_119_Agaricea_C3b C3b KF572337 Agaricia Agaricia agaricites Caribbean Barbados Atlantis Bank Reef Deep Bar05_133_Montastraea_C7a C7a KF572223 Orbicella Orbicella faveolata Caribbean Barbados Atlantis Bank Reef Deep Bar05_134_Montastraea_C7a C7a KF572224 Orbicella Orbicella faveolata Caribbean Barbados Atlantis Bank Reef Deep Bar05_135_Montastraea_C7a C7a KF572225 Orbicella Orbicella faveolata Caribbean Barbados Atlantis Bank Reef Deep Bar05_45_Palythoa_C1 C1 KF572179 Palythoa Palythoa caribaeorum Caribbean Barbados Bachelors Hall Shallow Bar05_75_Montastraea_C7a C7a KF572226 Orbicella Orbicella franksi Caribbean Barbados Atlantis Bank Reef Deep Bar05_80_Montastraea_C7a C7a KF572227 Orbicella Orbicella annularis Caribbean Barbados Atlantis Bank Reef Deep Bar05_84_Palythoa_C1 C1 KF572182 Palythoa Palythoa caribaeorum Caribbean Barbados Atlantis Bank Reef Deep
Cur11_20_Montastraea C7a KF572242 Orbicella Orbicella faveaolata Caribbean Curacao Intermediate Cur11_22_Montastraea C7a KF572243 Orbicella Orbicella faveaolata Caribbean Curacao Intermediate Cur11_23_Montastraea C7a KF572246 Orbicella Orbicella faveaolata Caribbean Curacao Intermediate Cur11_25_Montastraea C7a KF572241 Orbicella Orbicella faveaolata Caribbean Curacao Intermediate Cur11_27a_Montastraea C7a KF572244 Orbicella Orbicella faveaolata Caribbean Curacao Intermediate Cur11_27b_Montastraea C7a KF572245 Orbicella Orbicella faveaolata Caribbean Curacao Intermediate Cur11_44_Montastraea C7a KF572233 Orbicella Orbicella faveaolata Caribbean Curacao Intermediate Cur11_46_Montastraea C7a KF572234 Orbicella Orbicella faveaolata Caribbean Curacao Intermediate Cur11_47_Montastraea C7a KF572232 Orbicella Orbicella faveaolata Caribbean Curacao Intermediate CVX09_01_Palythoa_C1 C1 KF572184 Palythoa Palythoa caribaeorum East Atlantic Cape Verde Intermediate F1362_AG_Mfranksi2_C3 C3 KF572274 Orbicella Orbicella franksi Caribbean Florida Keys Alligator Reef Deep F1363_AG_M_franksi_C3 B1, C3 KF572276 Orbicella Orbicella franksi Caribbean Florida Keys Alligator Reef Deep F1377_AG_Mfranksi2_C3 C3 KF572275 Orbicella Orbicella franksi Caribbean Florida Keys Alligator Reef Deep F1378_AG_Mfranksi3_C3 C3 KF572272 Orbicella Orbicella franksi Caribbean Florida Keys Alligator Reef Deep F1379_AG_Mfranksi4_C3 C3 KF572273 Orbicella Orbicella franksi Caribbean Florida Keys Alligator Reef Deep F1380_AG_M_franksi_C3 C3 KF572277 Orbicella Orbicella franksi Caribbean Florida Keys Alligator Reef Deep FGB_70_Siderastrea C1 KF572160 Siderastrea Siderastrea siderea Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_17_Mussa_C3 C3 KF572281 Mussa Mussa angulosa Caribbean Flower Garden Banks West Bank-Bouy Deep FGB05_18_Mussa_C3 C3 KF572280 Mussa Mussa angulosa Caribbean Flower Garden Banks West Bank-Bouy Deep FGB05_30_C3_Leptoseris_C3 C3 KF572335 Leptoseris Leptoseris cucullata Caribbean Flower Garden Banks West Bank-Bouy Deep FGB05_31_C3_Leptoseris_C3 C3 KF572334 Leptoseris Leptoseris cucullata Caribbean Flower Garden Banks West Bank-Bouy Deep FGB05_32_C3_Leptoseris_C3 C3 KF572333 Leptoseris Leptoseris cucullata Caribbean Flower Garden Banks West Bank-Bouy Deep FGB05_34_Siderastrea C1 KF572157 Siderastrea Siderastrea siderea Caribbean Flower Garden Banks West Bank-Bouy Deep FGB05_35_Agaricia_C3s C3s KF572384 Agaricia Agaricia agaricites Caribbean Flower Garden Banks West Bank-Bouy Deep FGB05_39_Stephanocoenia_C87 C87 KF572416 Stephanocoenia Stephanocoenia intersepta Caribbean Flower Garden Banks West Bank-Bouy Deep FGB05_40_Stephanocoenia_C87 C87 KF572417 Stephanocoenia Stephanocoenia intersepta Caribbean Flower Garden Banks West Bank-Bouy Deep FGB05_53_Agaricia_C3s C3s KF572383 Agaricia Agaricia agaricites Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_54_Agaricia_C3s C3s KF572382 Agaricia Agaricia agaricites Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_55_Agaricia_C3s C3s KF572381 Agaricia Agaricia agaricites Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_64a_Mussa_C3 C3 KF572282 Mussa Mussa angulosa Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_65_Mussa_C3 C3 KF572279 Mussa Mussa angulosa Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_66_Mussa_C3 C3 KF572278 Mussa Mussa angulosa Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_67_Scolemia_C3 C3 KF572297 Scolemia Scolemia cubensis Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_69_Siderastrea C1 KF572158 Siderastrea Sideratrea siderea Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_76_Scolemia_C3 C3 KF572296 Scolemia Scolemia cubensis Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_78_Stephanocoenia_C87 C87 KF572418 Stephanocoenia Stephanocoenia intersepta Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_81_Agaricia_C3s C3s KF572380 Agaricia Agaricia agaricites Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_77_Stephanocoenia_C87 C87 KF572415 Stephanocoenia Stephanocoenia intersepta Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_89_Siderastrea C1 KF572156 Siderastrea Siderastrea siderea Caribbean Flower Garden Banks East Bank-Bouy Deep FGB05_90_Acropora C1 KF572159 Acropora Acropora palmata Caribbean Flower Garden Banks Deep FL01_31_C3_Erythropodium_C3 C3 KF572291 Erythropodium Erythropodium caribaeorum Caribbean Florida Keys Key Largo Intermediate FL01_35_Palythoa C1 KF572178 Palythoa Palythoa caribaeorum Caribbean Florida Keys Key Largo Shallow
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FL01_6_Agaricia_C3a C3a KF572399 Agaricia Agaricia agaricites Caribbean Florida Keys Key Largo Shallow FL01_8_Agaricia_C3b C3b KF572389 Agaricia Agaricia humilis Caribbean Florida Keys Key Largo Shallow FL02_63_Palythoa_C1 C1 KF572181 Palythoa Palythoa caribaeorum Caribbean Florida Keys Alligator Reef Deep FL02_81_Lebrunia C1 KF572168 Lebrunia Lebrunia danae Caribbean Florida Keys Admiral Reef Shallow FLKeys_6298_Acorpora1 C1 KF572153 Acropora Acropora cervicornis Caribbean Florida Keys Shallow FLKeys_6302_Acropora2 C1 KF572154 Acropora Acropora cervicornis Caribbean Florida Keys Shallow Haw02_113_C27 C27 JQ043668 Pavona Pavona duerdeni Central Pacific Oahu Kaneohe Bay Deep Haw02_18b_Montipora_31 C31 JQ043612 Montipora Montipora capitata Central Pacific Oahu Kaneohe Bay Shallow Haw02_23_C27 C27 JQ043667 Pavona Pavona varians Central Pacific Oahu North shore Deep Haw02_41_C27 C27 JQ043673 Pavona Pavona duerdeni Central Pacific Oahu North shore Deep Haw02_43_C27 C27 JQ043672 Pavona Pavona duerdeni Central Pacific Oahu North shore Deep Haw02_45b_Montipora_31 C31 KF572371 Montipora Montipora capitata Central Pacific Oahu North shore Deep Haw02_51_Fungia_C1bf C1bf KF572218 Fungia Fungia scutaria Central Pacific Oahu North shore Deep Haw02_5b_Montipora_C31 C31 JQ043613 Montipora Montipora capitata Central Pacific Oahu Kaneohe Bay Shallow Haw02_6_Fungia_C1bf C1bf KF572219 Fungia Fungia scutaria Central Pacific Oahu Kaneohe Bay, Shallow Haw02_63_Psammocora_C1bf C1bf KF572220 Psammocora Psammocora haimeana Central Pacific Oahu Kaneohe Bay Shallow Haw02_7_Fungia_C1bf C1bf KF572221 Fungia Fungia scutaria Central Pacific Oahu Kaneohe Bay, Shallow Haw02_73_C27 C27 JQ043671 Pavona Pavona varians Central Pacific Oahu Kaneohe Bay, Shallow Haw02_86_Cyphastrea_C1bf C1bf KF572217 Cyphastrea Cyphastrea ocellina Central Pacific Oahu Kaneohe Bay, Shallow Haw02_95_C27 C27 JQ043674 Pavona Pavona varians Central Pacific Oahu Kaneohe Bay, Shallow JPB08_08_Agaricea_C3b C3b KF572394 Agaricia Agaricia agaricites Northeastern Brazil Paraíba, João Pessoa Picãozinho Shallow JPB08_17_Siderastrea_C3 C3 KF572376 Siderastrea Siderastrea stellata Northeastern Brazil Paraíba, João Pessoa Picãozinho Shallow JPB08_19_Agaricea_C3b C3b KF572390 Agaricia Agaricia agaricites Northeastern Brazil Paraíba, João Pessoa Picãozinho Shallow JPB08_24_Siderastrea_C3 C3 KF572375 Siderastrea Siderastrea stellata Northeastern Brazil Paraíba, João Pessoa Picãozinho Shallow JPB08_31_Agaricea_C3b C3b KF572391 Agaricia Agaricia agaricites Northeastern Brazil Paraíba, João Pessoa Picãozinho Shallow JPB08_34_Protopalythoa C1 KF572170 Protopalythoa Protopalythoa variabilis Northeastern Brazil Paraíba, João Pessoa Picãozinho Shallow JPB08_35_Agaricea_C3b C3b KF572393 Agaricia Agaricia agaricites Northeastern Brazil Paraíba, João Pessoa Picãozinho Shallow JPB08_39_Protopalythoa_C1 C1 KF572177 Protopalythoa Protopalythoa variabilis Northeastern Brazil Paraíba, João Pessoa Cabo Branco Shallow JPB08_42_Palythoa C1 KF572171 Palythoa Palythoa caribeaorum Northeastern Brazil Paraíba, João Pessoa Cabo Branco Shallow JPB08_47_Protopalythoa_C1 C1 KF572176 Protopalythoa Protopalythoa variabilis Northeastern Brazil Paraíba, João Pessoa Cabo Branco Shallow JPB08_48_Protopalythoa_C1 C1 KF572175 Protopalythoa Protopalythoa variabilis Northeastern Brazil Paraíba, João Pessoa Cabo Branco Shallow JPB08_52_Agaricea_C3b C3b KF572392 Agaricia Agaricia agaricites Northeastern Brazil Paraíba, João Pessoa Cabo Branco Shallow JPB08_55_Porites_astreoides C1 KF572169 Porites Porites astreoides Northeastern Brazil Paraíba, João Pessoa Cabo Branco Shallow JPB08_6_Siderastrea_C3 C3 KF572377 Siderastrea Siderastrea stellata Northeastern Brazil Paraíba, João Pessoa Picãozinho Shallow JPB08_61_Siderastrea_C1 C1 KF572192 Siderastrea Siderastrea stellata Northeastern Brazil Baia da Traicao Shallow JPB08_63_Protopalythoa_C1 C1 KF572174 Protopalythoa Protopalythoa variabilis Northeastern Brazil Baia da Traicao Shallow JPB08_75_Isaurus_C1 C1 KF572198 Isaurus Isaurus sp. Southwest Brazil Praia do Forte Shallow JPB08_76_Siderastrea_C1 C1 KF572200 Siderastrea Siderastrea stellata Southwest Brazil Praia do Forte Shallow JPB08_77_Siderastrea_C1 C1 KF572201 Siderastrea Siderastrea stellata Southwest Brazil Praia do Forte Shallow JPB08_79_Siderastrea_C1 C1 KF572202 Siderastrea Siderastrea stellata Southwest Brazil Praia do Forte Shallow JPB08_82_Zoanthus_C1 C1 KF572196 Zoanthus Zoanthus sociatus Southwest Brazil Praia do Forte Shallow JPB08_84_Zoanthus_C1 C1 KF572191 Zoanthus Zoanthus sociatus Southwest Brazil Praia do Forte Shallow
7
JPB08_92_Siderastrea_C1 C1 KF572197 Siderastrea Siderastrea stellata Southwest Brazil Lauro de Freitas Shallow LB5_mexico_Montastraea_C7 C7 KF572249 Orbicella Orbicella faveolata Caribbean Mexico Puerto Morelos Shallow Montastraea_Cur11_31 C7 KF572261 Orbicella Orbicella faveolata Caribbean Curacao Playa Kalki Intermediate Montastraea_Cur11_66 C7 KF572250 Orbicella Orbicella annularis Caribbean Curacao Playa Largu Intermediate Montastraea_Cur11_67 C7 KF572251 Orbicella Orbicella franksi Caribbean Curacao Playa Largu Intermediate Montastraea_Cur11_68 C7 KF572252 Orbicella Orbicella franksi Caribbean Curacao Playa Largu Intermediate Montastraea_Cur11_72 C7 KF572253 Orbicella Orbicella franksi Caribbean Curacao Playa Largu Intermediate Montastraea_Cur11_73 C7 KF572262 Orbicella Orbicella faveolata Caribbean Curacao Playa Largu Intermediate Montastraea_Cur11_74 C7 KF572263 Orbicella Orbicella faveolata Caribbean Curacao Playa Largu Intermediate Montastraea_Cur11_75 C7 KF572264 Orbicella Orbicella faveolata Caribbean Curacao Playa Largu Intermediate Montastraea_Cur11_80 C7 KF572265 Orbicella Orbicella faveolata Caribbean Curacao Playa Largu Intermediate Montastraea_Cur11_81 C7 KF572266 Orbicella Orbicella faveolata Caribbean Curacao Playa Largu Intermediate Montastraea_Cur11_84 C7 KF572267 Orbicella Orbicella faveolata Caribbean Curacao Playa Largu Intermediate PM99_20_Isophyllastrea_C3 C3 KF572284 Isophyllastrea Isophyllastrea rigida Caribbean Puerto Morelos Shallow PM99_22_Leptoseris_C3 C3 KF572407 Leptoseris Leptoseris cucullata Caribbean Puerto Morelos Petem Deep PM99_29_Mycetophyllia_C3 C3 KF572419 Mycetophyllia Mycetophyllia lamarckiana Caribbean Puerto Morelos Petem Deep PM99_30_Mycetophyllia_C3 C3 KF572420 Mycetophyllia Mycetophyllia lamarckiana Caribbean Puerto Morelos Petem Deep PM99_31_Mycetophyllia_C3 C3 KF572421 Mycetophyllia Mycetophyllia sp. Caribbean Puerto Morelos Petem Deep PM99_32_Mycetophyllia_C3 C3 KF572353 Mycetophyllia Mycetophyllia sp. Caribbean Puerto Morelos Petem Deep PM99_33_Mycetophyllia_C3 C3 KF572422 Mycetophyllia Mycetophyllia danana Caribbean Puerto Morelos Petem Deep PM99_35_Porites_C1a_j C1aj KF572185 Porites Porites astreoides Caribbean Puerto Morelos Petem Deep PM99_36_Porites_C1a_j C1aj KF572186 Porites Porites astreoides Caribbean Puerto Morelos Petem Deep PM99_72_Discosoma_C1 C1 KF572199 Discosoma Discosoma carlgreni Caribbean Puerto Morelos Bocana Shallow PM99_73_Discosoma C1 KF572167 Discosoma Discosoma sanctithomae Caribbean Puerto Morelos Bocana Shallow PM99_74_C3_Ricordia_C3 C3 KF572287 Ricordea Ricordea florida Caribbean Puerto Morelos Petem Deep RB38_Palythoa_C1 C1 KF572183 Palythoa Palythoa caribaeorum Caribbean Barbados Reef Balls Deep SPA45_Montipora_C31 C31 JQ043602 Montipora Montipora sp. Indo-Pacific Aquarium trade N.A. N.A. SPA59_SW2_Montipora_C31c C31c JQ043601 Montipora Montipora capitata Indo-Pacific Aquarium trade N.A. N.A. STX04_15_Siderastrea_C3 C3 KF572308 Siderastrea Siderastrea siderea Caribbean St. Croix leeward side Shallow STX04_31_Montastraea_C7a C7a KF572228 Orbicella Orbicella annularis Caribbean St. Croix leeward side Deep STX04_32_Montastraea_C7a C7a KF572229 Orbicella Orbicella franksi Caribbean St. Croix leeward side Deep STX04_34_Montastraea_C7a C7a KF572230 Orbicella Orbicella faveolata Caribbean St. Croix leeward side Deep STX04_35_Montastraea_C7a C7a KF572231 Orbicella Orbicella faveolata Caribbean St. Croix leeward side Deep STX04_36_Stephanocoenia C16a KF572348 Stephanocoenia Stephanocoenia intersepta Caribbean St. Croix leeward side Deep STX04_37_Stephanocoenia C16a KF572349 Stephanocoenia Stephanocoenia intersepta Caribbean St. Croix leeward side Deep STX04_54a_Siderastrea_C3 C3 KF572309 Siderastrea Siderastrea siderea Caribbean St. Croix leeward side Deep STX04_55a_Siderastrea_C3 C3 KF572310 Siderastrea Siderastrea siderea Caribbean St. Croix leeward side Deep STX04_58_Agaricia_C3 C3 KF572411 Agaricia Agaricia agaricities Caribbean St. Croix leeward side Deep STX04_59_Agaricia_C3 C3 KF572412 Agaricia Agaricia agaricities Caribbean St. Croix leeward side Deep STX04_61_Agaricia_C3 C3 KF572410 Agaricia Agaricia agaricities Caribbean St. Croix leeward side Deep SW37_Pectinia_C40 C40 KF572369 Pectinia Pectinia sp. Indo-Pacific Aquarium trade N.A. N.A. WA10_Cyphastrea_C40 C40 KF572364 Cyphastrea Cyphastrea chalcidicum Western Australia Ningaloo Reef Intermediate
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WA112_Hydnophora_C40 C40 KF572366 Hydnophora Hydnophora rigida Western Australia Ningaloo Reef Intermediate WA29_Echinophora_C40 C40 KF572367 Echinopora Echinopora lamellosa Western Australia Ningaloo Reef Intermediate WA908_Acropora_C40 C40 KF572362 Acropora Acropora latistella Western Australia Dampier Intermediate WA93_Hydnophora_C40 C40 KF572368 Hydnophora Hydnophora rigida Western Australia Ningaloo Reef Intermediate WA99_Cyphastrea_C40 C40 KF572365 Cyphastrea Cyphastrea chalcidicum Western Australia Ningaloo Reef Intermediate YBD3_Montastraea_C7 C7 KF572259 Orbicella Orbicella faveolata Caribbean Panama San Blas Intermediate YBD4_Montastraea_C7 C7 KF572260 Orbicella Orbicella faveolata Caribbean Panama San Blas Intermediate YBD59_Montastraea_C7 C7 KF572258 Orbicella Orbicella faveolata Caribbean Panama San Blas Intermediate 98_78_Montastraea_C7 C7 KF572255 Orbicella Orbicella faveolata Caribbean Panama San Blas Intermediate 98_79_Montastraea_C7 C7 KF572256 Orbicella Orbicella faveolata Caribbean Panama San Blas Intermediate 98_80_Montastraea_C7 C7 KF572257 Orbicella Orbicella faveolata Caribbean Panama San Blas Intermediate 98_83_Montastraea_C7c C7c KF572236 Orbicella Orbicella faveolata Caribbean Panama San Blas Intermediate 98_84_Montastraea_C7c C7c KF572235 Orbicella Orbicella faveolata Caribbean Panama San Blas Intermediate Zam03_10M_28_Alveopora_C27 C27 JQ043670 Pachyseris Pachyseris speciosa West Pacific Ryukyus Isls. Zamami Island Intermediate Zam03_10M_33_Alveopora_C27 C27 JQ043669 Alveopora Alveopora sp. West Pacific Ryukyus Isls. Zamami Island Intermediate Zam03_10m_68_Montipora_C31 C31 JQ043599 Montipora Montipora sp. West Pacific Ryukyus Isls. Zamami Island Intermediate Zam03_10m_87_Montipora_C31 C31 JQ043604 Montipora Montipora venosa West Pacific Ryukyus Isls. Zamami Island Intermediate Zam03_3m_87_Montipora_C31 C31 JQ043603 Montipora Montipora sp. West Pacific Ryukyus Isls. Zamami Island Shallow Zam03_3m_92_Montipora_C30 C30 JQ043605 Montipora Montipora efflorescens West Pacific Ryukyus Isls. Zamami Island Shallow Zam03_3m_95_Montipora_C31 C31 JQ043600 Montipora Montipora capitata West Pacific Ryukyus Isls. Zamami Island Shallow Zam03_3m_25_Astreopora_C1 C1 KF572206 Astreopora Astreopora myriophthalma West Pacific Ryukyus Isls. Zamami Island Shallow Zam03_41_Fungia_C27 C27 JQ043676 Fungia Fungia sp. West Pacific Ryukyus Isls. Zamami Island Shallow
Table S2. Summary statistics on allele number and evenness among unique multilocus genotypes representing Symbiodinium lineages associated with Orbicella and Siderastrea from the Greater Caribbean of the western Atlantic. Standard error (numbers in smaller font) is given below each mean. C7 C7a/C12 C3Siderastrea Nunique 31 14 33 Na 3.200 3.400 7.100 0.573 0.600 0.767 Ae 2.055 2.356 3.697 0.347 0.412 0.442 Ho 0.000 0.000 0.599 0.000 0.000 0.077 He 0.377 0.445 0.673 0.094 0.090 0.057
Na = Average no. of alleles per locus Ae = No. of effective alleles per locus [1 / (Sum pi^2)] Ho = Observed heterozygosity [No. of Hets / N] He = Expected heterozygosity [1 - Sum pi^2]