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Supplementary Material

Fine-scale biogeographical boundary delineation and sub-population resolution in the Symbiodinium thermophilum coral symbiont group

from the Persian / Arabian Gulf and Gulf of Oman

Benjamin C.C. Hume

1,2*

, Cecilia D’Angelo

2,4

, John Burt

3

& Jörg Wiedenmann

2,4

* Correspondence: Benjamin C C Hume: [email protected]

1 Supplementary Figures and Tables

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Table S1: PsbAncr sequences used in the construction of the maximum parsimony network.

ID Collection Site Collection

Date

Accession Number

Host Species ID Collection Site Collection Date

Accession Number

Host Species

BH1415 Dalma Sept 2012 KM458276 P. harrisoni BH1668 Umm Al Quwain March 2013 KP280258 P. lutea

BH1448 Dalma Sept 2012 KM458286 P. harrisoni BH1456 Umm Al Quwain March 2013 KM458291 P. lutea

BH1413 Dalma Sept 2012 KM458274 P. harrisoni BH1669 Umm Al Quwain March 2013 KP280260 P. lutea

BH1414 Dalma Sept 2012 KM458275 P. harrisoni BH1457 Umm Al Quwain March 2013 KP280261 P. lutea

BH1450 Dalma Sept 2012 KM458288 P. lutea BH1660 Umm Al Quwain March 2013 KP280262 P. lutea

BH1449 Dalma Sept 2012 KM458287 P. lutea BH1392 Umm Al Quwain March 2013 KM458294 P. lutea

BH1692 Dalma Sept 2012 KP280211 P. lutea BH1458 Umm Al Quwain March 2013 KM458292 P. lutea

BH1690 Dalma Sept 2012 KP280212 P. harrisoni BH1427 Umm Al Quwain March 2013 KM458284 P. lutea

BH1643 Dalma Sept 2012 KP280213 P. harrisoni BH1679 Umm Al Quwain March 2013 KP280265 P. lutea

BH1411 Dalma Sep 2012 KM458273 P. harrisoni BH1688 Umm Al Quwain March 2013 KP280266 P. lutea

BH1647 Dalma Sept 2012 KP280215 P. harrisoni BH1675 Ras Al-Kaimah March 2013 KP280267 Porites sp.

BH1691 Dalma Sept 2012 KP280216 P. harrisoni BH1621 Ras Al-Kaimah March 2013 KP280268 Porites sp.

BH1447 Dalma Sept 2012 KP280217 P. harrisoni BH1671 Ras Al-Kaimah March 2013 KP280269 Porites sp.

BH1693 Dalma Sept 2012 KP280218 P. lutea BH1672 Ras Al-Kaimah March 2013 KP280270 Porites sp.

BH1416 Dalma Sept 2012 KP280219 P. harrisoni BH1676 Ras Al-Kaimah March 2013 KP280271 Porites sp.

BH1702 Saadiyat Sept 2012 KP280220 P. lobata BH1623 Ras Al-Kaimah March 2013 KP280272 Porites sp.

BH1704 Saadiyat Sept 2012 KP280221 P. lobata BH1620 Ras Al-Kaimah March 2013 KP280273 Porites sp.

BH1708 Saadiyat Sept 2012 KP280222 P. lobata BH1624 Ras Al-Kaimah March 2013 KP280275 Porites sp.

BH1356 Saadiyat Sept 2012 KM458293 P. lutea BH1670 Ras Al-Kaimah March 2013 KP280276 Porites sp.

BH1422 Saadiyat Sept 2012 KM458279 P. lutea BH1673 Ras Al-Kaimah March 2013 KP280277 Porites sp.

BH1451 Saadiyat Sept 2012 KM458289 P. lobata BH1678 Ras Al-Kaimah March 2013 KP280278 Porites sp.

BH1417 Saadiyat Sept 2012 KM458277 P. lutea BH1680 Ras Al-Kaimah March 2013 KP280279 Porites sp.

BH1419 Saadiyat Sept 2012 KM458278 P. lutea BH1677 Ras Al-Kaimah March 2013 KP280280 Porites sp.

BH1699 Saadiyat Sept 2012 KP280227 P. lutea BH1683 Ras Al-Kaimah March 2013 KP280281 Porites sp.

BH1701 Saadiyat Sept 2012 KP280228 P. lutea BH1497 Ras Al-Kaimah March 2013 KP280282 Porites sp.

BH1705 Saadiyat Sept 2012 KP280229 P. lutea BH1625 Ras Al-Kaimah March 2013 KP280283 Porites sp.

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BH1706 Saadiyat Sept 2012 KP280230 P. lutea BH1682 Ras Al-Kaimah March 2013 KP280284 Porites sp.

B315 Saadiyat Sept 2012 KP280231 P. harrisoni BH1681 Ras Al-Kaimah March 2013 KP280285 Porites sp.

BH1696 Saadiyat Sept 2012 KP280232 P. harrisoni BH1674 Ras Al-Kaimah March 2013 KP280286 Porites sp.

BH1641 Saadiyat Sept 2012 KP280233 P. lobata B21549 Musandam March 2013 KP280287 P. lobata

BH1703 Saadiyat Sept 2012 KP280234 P. harrisoni B21550 Musandam March 2013 KP280288 P. lobata

BH1642 Saadiyat Sept 2012 KP280235 P. harrisoni BH1652 Musandam March 2013 KP280289 P. lobata

BH1698 Saadiyat Sept 2012 KP280236 P. lutea BH1616 Musandam March 2013 KP280290 P. lutea

BH1487 Saadiyat Sept 2012 KP280237 P. lobata BH1617 Musandam March 2013 KP280291 P. lobata

BH1639 Saadiyat Sept 2012 KP280239 P. lutea B21551 Musandam March 2013 KP280292 P. lutea

BH1700 Saadiyat Sept 2012 KP280240 P. harrisoni B21552 Musandam March 2013 KP280293 P. lutea

BH1453 Saadiyat Sept 2012 KM458290 P. lobata B21553 Musandam March 2013 KP280294 P. lutea

BH1636 Ras Ghanada Sept 2012 KP280242 P. lutea B21554 Musandam March 2013 KP280295 P. lutea

BH1547 Ras Ghanada Sept 2012 KP280243 P. lobata BH1649 Musandam March 2013 KP280296 P. lobata

BH1632 Ras Ghanada Sept 2012 KP280244 P. lobata BH1653 Musandam March 2013 KP280297 P. lutea

BH1634 Ras Ghanada Sept 2012 KP280245 P. harrisoni BH1655 Musandam March 2013 KP280298 P. lutea

BH1635 Ras Ghanada Sept 2012 KP280246 P. harrisoni B341 Musandam March 2013 KP280299 P. lutea

BH1548 Ras Ghanada Sept 2012 KP280247 P. lutea BH1659 Musandam March 2013 KP280300 P. lutea

BH1631 Ras Ghanada Sept 2012 KP280248 P. harrisoni B21556 Musandam March 2013 KP280301 P. lobata

BH1633 Ras Ghanada Sept 2012 KP280249 P. harrisoni BH1658 Musandam March 2013 KP280302 P. lobata

BH1664 Umm Al Quwain March 2013 KP280250 P. lutea B21557 Musandam March 2013 KP280303 P. lobata

BH1425 Umm Al Quwain March 2013 KM458282 P. lutea BH1656 Musandam March 2013 KP280304 P. lobata

BH1662 Umm Al Quwain March 2013 KP280252 P. lutea BH1614 Musandam March 2013 KP280305 P. lobata

BH1428 Umm Al Quwain March 2013 KM458285 P. lutea BH1615 Musandam March 2013 KP280306 P. lobata

BH1424 Umm Al Quwain March 2013 KM458281 P. lutea B21561 Fujairah Sept 2012 KP280307 P. lobata

BH1628 Umm Al Quwain March 2013 KP280255 P. lutea BH1550 Fujairah Sept 2012 KP280308 P. lobata

BH1426 Umm Al Quwain March 2013 KM458283 P. lutea B21560 Fujairah Sept 2012 KP280309 P. lobata

BH1423 Umm Al Quwain March 2013 KM458280 P. lutea B334 Fujairah Sept 2012 KP280310 P. lobata

Sequences with accession numbers beginning KM are from: Hume et al. 2015 and represent the samples used to define Symbiodinium thermophilum.

Sequences with accession numbers beginning KP are from D’Angelo et al. 2015.

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Table S2: Number of samples and depth of sequencing for the nrDNA marker

Collection Site Colonies Collected Average clones sequenced per coral colony

Dalma 5 8

Saadiyat 23 6

Ras Ghanada 4 6

Umm Al Quwain 4 11

Ras Al-Kaimah 6 8

Musandam West 4 7

Musandam East 3 6

Fujairah 12 6

Muscat 1 14

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Table S3: Distance matrix used in Mantel tests (km).

DAL SAD RAG UMM RAK MW ME FUJ MUC

DAL 0

SAD 230 0

RAG 268 38 0

UMM 400 170 132 0

RAK 439 209 171 39 0

MW 494 264 226 94 55 0

ME 516 286 248 106 77 22 0

FUJ 634 404 366 234 195 140 118 0

MUC 997 767 729 597 558 503 481 363 0

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Figure S1: Aqua MODIS SST (11 µ daytime) August climatology 2002-2015.

Figure S2: Sampling frequencies by site and species. For the rDNA marker, given the cloning strategy employed in this study, sampling frequencies are given both by total number of sequences returned and number of corals sampled, both by site and species.

2 Code S1: Mothur, R and Python scripts

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Example Mothur, R and Python scripts used in this study are available at https://github.com/didillysquat/PAG-Code

3 References

D'Angelo, C., Hume, B.C.C., Burt, J., Smith, E.G., Achterberg, E.P., and Wiedenmann, J. (2015).

Local adaptation constrains the distribution potential of heat-tolerant Symbiodinium from the Persian/Arabian Gulf. ISME J 9, 2551-2560. doi: 10.1038/ismej.2015.80.

Hume, B.C.C., D'Angelo, C., Smith, E.G., Stevens, J.R., Burt, J., and Wiedenmann, J. (2015).

Symbiodinium thermophilum sp nov., a thermotolerant symbiotic alga prevalent in corals of the world's hottest sea, the Persian/Arabian Gulf. Scientific Reports 5. doi:

10.1038/srep08562.

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