ESM Table S1. List of Forward and Reverse Primers for Mitochondrial and Nuclear DNA Markers

ESM Table S1. List of Forward and Reverse Primers for Mitochondrial and Nuclear DNA Markers

ESM Table S1. List of forward and reverse primers for mitochondrial and nuclear DNA markers used during screening. Only the Cytochrome-c Oxidase subunit-I and S7 markers were used for analyses. Amplification was considered unsuccessful where PCR resulted in amplification of < 50% of the samples as visualized on a 1.5 % agarose gel.

Mitochondrial gene / Reference / Forward primer / Reverse primer / Outcome
12S / Palumbi (1996) / 12Sa
AAACTGGGATTATAGACCCCACTAT / 12Sb
GAGGGTGACGGGCGGTCTCT / Amplification unsuccessful
16S / Palumbi (1996) / 16Sar-L
GCCTGTTTATCAAAAACAT / 16Sbr-H
CCGGTCTGAACTCAGATCAGT / Amplified with no fixed differences
Cytochrome Oxidase 1 (COI) / Ward et al. (2005) / F2
CGACTAATC ATAAAGATATCGGCAC / R2
ACTTCAGGGTGACCGAAGAATCAGAA / Amplified with no fixed differences
Control Region (CR) / Lee et al. (1995) / CRA
TTCCACCTCTAACTCCCAAAGCTAG / CRE
ACGCTGGAAAGAACGCCCGGCATGG / Amplified with no fixed differences
Cytochrome B (CYT-B) / HS: Song et al. (1998)
LS: Taberlet et al. (1992) / HS GTGACTTGAAAAACCACCGTTG / LS
AATAGGAAGTATCATTCGGGTTTGATG / Amplification unsuccessful
Nuclear gene / Reference / Forward primer / Reverse primer / Outcome
36298E1 / Li et al. (2010) / 36298E1-F
GATCCTGAGGGAYTCCCAYGGTGT / 36298E1-R
GGCCAGGACTCTCYTGGTCTTGTAGT / Amplified with no fixed differences
ETS2 / Dolman and Phillips (2004) / ETS2F
AGCTGTGGCAGTTTCTTCTG / ETS2R
CGGCTCAGCTTCTCGTAG / Amplified with no fixed differences
TMO 4C4 / Streelman and Karl (1997) / TMO-F1
CCTCCGGCCTTCCTAAAACCTCTC / TMO-R1
CATCGTGCTCCTGGGTGACAAAGT / Amplified with no fixed differences
Histone 3 (H3) / Colgan et al. (1998) / H3A-L
ATGGCTCGTACCAAGCAGACVGC / H3B
ATATCCTTRGGCATRATRGTGAC / Amplification unsuccessful
S7 / Chow and Hazama (1998) / S7RPEX1F
TGGCCTCTTCCTTGGCCGTC / S7RPEX2R
AACTCGTCTGGCTTTTCGCC / Amplified with no fixed differences
Recombination Activating Gene 2
(RAG2) / Westneat and Alfaro (2005) / F1
GAGGGCCATCTCCTTCTCCAA / R3
GATGGCCTTCCCTCTGTGGGTAC / Amplification unsuccessful
Recombination Activating Gene 2
(RAG2 – Modified) / DiBattista et al. (2012) / RAG2 2F
SACCTTGTGCTGCAAAGAGA / RAG2 2R
GGATCCCCTTBTCATCCAGA / Amplification unsuccessful

References

Chan TTC, Sadovy Y (2002) Reproductive biology, age and growth in the chocolate hind, Cephalopholis boenak (Bloch, 1790), in Hong Kong. Mar Freshw Res 53:791–803

Chow S, Hazama K (1998) Universal PCR primers for S7 ribosomal protein gene introns in fish. Mol Ecol 7:1247–1263

Colgan DJ, McLauchlan A, Wilson GDF, Livingson SP, Edgecombe GD, Macaranas J, Cassis G, Gray MR (1998) Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Aust J Zool 46:419–437

de Araujo JN, Martins AS (2006) Age and growth of coney (Cephalopholis fulva), from the central coast of Brazil. J Mar Biol Assoc UK 1:187– 191

DiBattista JD, Waldrop E, Bowen BW, Schultz JK, Gaither MR, Pyle RL, Rocha LA (2012) Twisted sister species of pigmy angelfishes: discordance between taxonomy, colouration, and phylogenetics. Coral Reefs 31:839–851

Dolman G, Phillips B (2004) Single copy nuclear DNA markers characterized for comparative phylogeography in Australian wet tropics rainforest skinks. Mol Ecol 4:185–187

Lee WJ, Howell WH, Kocher TD (1995) Structure and evolution of teleost mitochondrial control regions. J Mol Evol 41:54–66

Li C, Riethovan JM, Ma L (2010) Exon-primed intron-crossing (EPIC) markers for non-model teleosts fishes. BMC Evol Biol 10:90–102

Palumbi S (1996) Nucleic acids II: The polymerase chain reaction. Mol Syst 10:205–248

Song CB, Near TJ, Page LM (1998) Phylogenetic relations among percid fishes as inferred from mitochondrial cytochrome b DNA sequence data. Mol Phylogenet Evol 10:343–353

Streelman JT, Karl SA (1997) Reconstructing labroid evolution with single-copy nuclear DNA. Proc R Soc Lond Biol Sci 264:1011–1020

Taberlet P, Meyer A, Bouvert J (1992) Unusually large mitochondrial variation in populations of the blue tit, Parus caeruleus. Mol Ecol 1:27–36

Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B Biol Sci 360:1847–1857

Westneat MW, Alfaro MA (2005) Phylogenetic relationships and evolutionary history of the reef fish family Labridae. Mol Phylogenet Evol 36:370–390

ESM Table S2. Descriptions of micro-habitat categories used to classify substrates along point intercept transects at Christmas Island. Descriptions based on Eagle et al. (2001) and Hobbs et al. (2010).

Micro-habitat / Description
Calcareous algae / Hard, substrate encrusting coral that is often pink in colour
Branching corals / Arborescent, columnar and digitate scleractinian corals
Massive corals / Spherical, hemispherical and mount shape scleractinian corals
Tabular corals / Laminar or Plating scleractinian corals
Foliaceous corals / Thin leafy scleractinian corals that form irregular shapes and whirls
Corymbose corals / Bushy shaped scleractinian coral with branches extending from a single stem
Encrusting corals / Scleractinian corals that grow as a thin veneer on the substrate
Sand / Calcareous or silicious grains
Bare rubble / Segments of dead coral that are not yet covered in live algae or other live corals
Soft corals / Alcyonarian corals that lack a hard calcium carbonate skeleton
Turf algae / Epilithic algae that grows on the surface of rocky substrates and dead coral

References

Eagle JV, Jones GP, McCormick MI (2001) A multi-scale study of the relationships between habitat use and the distribution and abundance patterns of three coral reef angelfishes (Pomacanthidae). Mar Ecol Prog Ser 214:253–265

Hobbs JPA, Jones GP, Munday PL (2010) Rarity and extinction risk in coral reef angelfishes on isolated islands: interrelationships among abundance, geographic range size and specialization. Coral Reefs 29:1–11

ESM Table S3. Resemblance matrix of percent (%) cover of benthic micro-habitat variables based on point intercept transects conducted at Christmas and Cocos-Keeling Islands. * indicates correlations between benthic micro-habitat variables which were >70%.

Branching corals / Tabular corals / Corymbose / Massive corals / Foliaceous corals / Encrusting / Calcareous algae / Turf algae / Sand / Bare rubble / Soft corals
Branching corals / - / - / - / - / - / - / - / - / - / - / -
Tabular corals / -0.29549 / - / - / - / - / - / - / - / - / - / -
Corymbose corals / -0.19706 / 0.208336 / - / - / - / - / - / - / - / - / -
Massive corals / -0.17782 / 0.533066 / 0.466315 / - / - / - / - / - / - / - / -
Foliaceous corals / -0.16768 / 0.382442 / 0.215824 / 0.310723 / - / - / - / - / - / - / -
Encrusting corals / 0.190019 / 0.079912 / 0.372868 / 0.540375 / 0.036816 / - / - / - / - / - / -
Calcareous algae / 0.055206 / 0.146366 / 0.494969 / 0.420176 / 0.067611 / 0.369987 / - / - / - / - / -
Turf algae / -0.28058 / -0.40195 / -0.47524 / -0.75361 * / -0.42714 / -0.75616 * / -0.5244 / - / - / - / -
Sand / -0.05119 / 0.108055 / -0.24378 / -0.12203 / -0.06534 / -0.06267 / -0.17397 / -0.06478 / - / - / -
Bare rubble / 0.38191 / -0.04915 / -0.10103 / 0.072596 / 0.397527 / 0.113938 / -0.30551 / -0.34408 / 0.175139 / - / -
Soft corals / 0.259526 / -0.1667 / 0.182873 / -0.16511 / -0.25485 / 0.002548 / 0.155288 / 0.029517 / -0.26879 / -0.11019 / -