Data from: Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo‐Pacific octocoral family Xeniidae

McFadden CS, Gonzalez A, Imada R, Shi SS, Hong P, Ekins M, Benayahu Y

Date Published: April 16, 2019

DOI: https://doi.org/10.5061/dryad.5r59p06

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Title McFadden_suppl_164taxa_concatenated_alignment
Downloaded 2 times
Description Alignment of concatenated mtMutS + igr1 + COI + 28S rDNA barcodes for 164 taxa used to construct neighbor-joining tree (Kimura 2-parameter). Taxon abbreviations can be found in Appendix S1, Table S1 of the publication.
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Title McFadden_suppl_170taxa_concatenated_alignment
Downloaded 2 times
Description Alignment of concatenated mtMutS + igr1 + COI + 28S rDNA barcodes for 170 taxa used to construct maximum likelihood tree. Taxon abbreviations can be found in Appendix S1, Table S1 of the publication.
Download McFadden_suppl_170taxa_concatenated_alignm...nexus (396.4 Kb)
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Title McFadden_suppl_NJtree_164taxa_concatenatedgenes
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Description Neighbor-joining tree (Kimura 2-parameter) for 164 taxa constructed using concatenated mtMutS + igr1 + COI + 28S rDNA barcodes. Taxon abbreviations can be found in Appendix S1, Table S1 of the publication. With bootstrap percentages (1000 replicates). Newick format.
Download McFadden_suppl_NJtree_164taxa_concatenate...es.nwk (11.07 Kb)
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Title McFadden_suppl_MLtree_170taxa_concatenatedgenes
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Description Maximum likelihood tree for 170 taxa constructed using concatenated mtMutS + igr1 + COI + 28S rDNA barcodes. Taxon abbreviations can be found in Appendix S1, Table S1 of the publication. GTR+I+G model of evolution with 100 bootstrap replicates. Saved as .tre format.
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Title pairwise_distance_matrix_ln(km)
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Description Matrix of pairwise great circle distances (ln(kilometers)) among sampled sites. Site abbreviations: ISR: Eilat, Israel; SAU: Saudi Arabia, central Red Sea; MAD: Nosy Bé, Madagascar; NIN: Ningaloo Reef, Western Australia; KIM: Kimberley, Western Australia; SUL: Lembeh Strait, Sulawesi, Indonesia; PAL: Republic of Palau; DON: Dongsha Atoll, Taiwan; GRE: Green (Ludao) Is., Taiwan; YON: Yonaguni Is., Ryukyu Archipelago, Japan; LIZ: Lizard Is., Queensland, Australia; COR: Coral Sea Islands Territory, Australia; HER: Heron Is., Queensland, Australia. Saved in .csv format
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Title pairwise_diversity_and_distance_measures
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Description Pairwise values of compositional and phylogenetic beta-diversity indices among sampled sites. Indices were calculated using the 'betapart' R package (Baselga 2012).
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Title community_matrix
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Description Presence/absence matrix of molecular operational taxonomic units (MOTUs) by site. MOTUs determined by 0.3% genetic distance threshold. Site abbreviations: ISR: Eilat, Israel; SAU: Saudi Arabia, central Red Sea; MAD: Nosy Bé, Madagascar; NIN: Ningaloo Reef, Western Australia; KIM: Kimberley, Western Australia; SUL: Lembeh Strait, Sulawesi, Indonesia; PAL: Republic of Palau; DON: Dongsha Atoll, Taiwan; GRE: Green (Ludao) Is., Taiwan; YON: Yonaguni Is., Ryukyu Archipelago, Japan; LIZ: Lizard Is., Queensland, Australia; COR: Coral Sea Islands Territory, Australia; HER: Heron Is., Queensland, Australia.
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When using this data, please cite the original publication:

McFadden CS, Gonzalez A, Imada R, Shi SS, Hong P, Ekins M, Benayahu Y (2019) Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo‐Pacific octocoral family Xeniidae. Journal of Biogeography. https://doi.org/10.1111/jbi.13543

Additionally, please cite the Dryad data package:

McFadden CS, Gonzalez A, Imada R, Shi SS, Hong P, Ekins M, Benayahu Y (2019) Data from: Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo‐Pacific octocoral family Xeniidae. Dryad Digital Repository. https://doi.org/10.5061/dryad.5r59p06
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