DOI: 10.5061/dryad.d4152
title: Data from: Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella

description: Human-induced environmental changes have ushered in the rapid decline of
 coral reef ecosystems, particularly by disrupting the symbioses between
 reef-building corals and their photosymbionts. However, escalating
 stressful conditions enable some symbionts to thrive as opportunists. We
 present evidence that a stress-tolerant “zooxanthella” from the
 Indo-Pacific Ocean, Symbiodinium trenchii, has rapidly spread to coral
 communities across the Greater Caribbean. In marked contrast to
 populations from the Indo-Pacific, Atlantic populations of S. trenchii
 contained exceptionally low genetic diversity, including several
 widespread and genetically similar clones. Colonies with this symbiont
 tolerate temperatures 1–2 °C higher than other host–symbiont combinations;
 however, calcification by hosts harboring S. trenchii is reduced by nearly
 half, compared with those harboring natives, and suggests that these new
 symbioses are maladapted. Unforeseen opportunism and geographical
 expansion by invasive mutualistic microbes could profoundly influence the
 response of reef coral symbioses to major environmental perturbations but
 may ultimately compromise ecosystem stability and function.
description: R-script for the
 analysis Symbiodinium trenchii in the CaribbeanSource code for the
 analysis of observed pairwise genetic difference (PWD), expected PWD under
 panmixia, and permutation test for departure from expected pairwise
 genetic difference for microsatellite MLGs datasets from a population of
 S. trenchii in the Greater Caribbean, West Atlantic
 Ocean.PWD
 analysis S.trenchii Caribbean.RR-script for the
 analysis Symbiodinium trenchii in the Andaman Sea
 (Thailand)Source code for the
 analysis of observed pairwise genetic difference (PWD), expected PWD under
 panmixia, and permutation test for departure from expected pairwise
 genetic difference for microsatellite MLGs datasets from a population of
 S. trenchii in the Andaman Sea (Thailand), Eastern Indian
 Ocean.PWD
 analysis S.trenchii Thailand.RR-script for the
 analysis Symbiodinium trenchii in the Western Pacific
 (PalauSource code for the
 analysis of observed pairwise genetic difference (PWD), expected PWD under
 panmixia, and permutation test for departure from expected pairwise
 genetic difference for microsatellite MLGs datasets from a population of
 S. trenchii in the West Pacific Ocean (Palau).PWD analysis S.trenchii
 Palau.RR-script for the
 analysis Symbiodinium type A3 in the Eastern CaribbeanSource code for the
 analysis of observed pairwise genetic difference (PWD), expected PWD under
 panmixia, and permutation test for departure from expected pairwise
 genetic difference for microsatellite MLGs datasets from a population of
 Symbiodinium A3 (S. ‘fitti’ nomen nudum) in the Eastern Caribbean, West
 Atlantic Ocean.PWD analysis Sym. A3 East
 Carib.RR-script for the
 analysis Symbiodinium type B7 in the CaribbeanSource code for the
 analysis of observed pairwise genetic difference (PWD), expected PWD under
 panmixia, and permutation test for departure from expected pairwise
 genetic difference for microsatellite MLGs datasets from a population of
 Symbiodinium B7 from corals in the genus Madracis in the Caribbean, West
 Atlantic Ocean.PWD analysis Sym. B7
 Caribbeanwide.RR-script for the
 analysis Symbiodinium type C7 in the western CaribbeanSource code for the
 analysis of observed pairwise genetic difference (PWD), expected PWD under
 panmixia, and permutation test for departure from expected pairwise
 genetic difference for microsatellite MLGs datasets from a population of
 Symbiodinium C7 in the Western Caribbean (Belize), West Atlantic
 Ocean.PWD
 analysis Sym. C7 Belize.RR-script for the
 analysis Symbiodinium type D1 ‘S. glynni’ in the Eastern
 PacificSource code for the
 analysis of observed pairwise genetic difference (PWD), expected PWD under
 panmixia, and permutation test for departure from expected pairwise
 genetic difference for microsatellite MLGs datasets from a population of
 Symbiodinium ‘glynni’ (nomen nudum, = type D1) in the Gulf of California
 (La Paz), Eastern Pacific Ocean.PWD analysis Sym. D1 Gulf of
 California.RSymbiodinium trenchii
 CaribbeanExcel data files of
 multilocus genotypes (MLGs) based on microsatellites for Symbiodinium
 trenchii in the CaribbeanSymbiodinium trenchii
 ThailandExcel data files of
 multilocus genotypes (MLGs) based on microsatellites for Symbiodinium
 trenchii in the Andaman Sea (Thailand)Symbiodinium trenchii
 PalauExcel data files of
 multilocus genotypes (MLGs) based on microsatellites for Symbiodinium
 trenchii in the Western Pacific (Palau)Symbiodinium type
 A3_East CaribExcel data files of
 multilocus genotypes (MLGs) based on microsatellites for Symbiodinium type
 A3 in the Eastern CaribbeanSymbiodinium type B7
 CaribbeanExcel data files of
 multilocus genotypes (MLGs) based on microsatellites for Symbiodinium type
 B7 in the Caribbean.Symbiodinium type C7
 BelizeExcel data files of
 multilocus genotypes (MLGs) based on microsatellites for Symbiodinium type
 C7 in the western Caribbean.Symbiodinium type D1
 Gulf of CaliforniaExcel data files of
 multilocus genotypes (MLGs) based on microsatellites for Symbiodinium type
 D1 ‘S. glynni’ in the Eastern Pacific.Symbiodinium type D1 gulf of
 california.csv