Electronic supplementary material
Additional information regarding natural history of focal species
The four reef fish species chosen for this study vary in life history traits that may affect dispersal in reef fishes (Riginos and Victor 2001) including egg type, pelagic larval duration (PLD), and larval behavior. The species predicted to be the most philopatric was Apogon (Ostorhinchus) doederleini. A. doederleini are mouthbrooders and hold their eggs in the oral cavity until the larvae hatch and become competent (Takeyama et al.
2007). A. doederleini have a PLD of 16 – 27 days
(Gerlach et al.
2007). As larvae, they have a very strong homing instinct which makes self-recruitment back to the natal population highly likely (Atema et al.
2002; Gerlach et al.
2007). Although the larvae are weak swimmers (Leis and Carson-Ewart 1997), they are often able to resist prevailing currents away from the natal reef (Armsworth
2000; Gerlach et al.
2007). For this reason it has been hypothesized that larvae of this species generally complete development close to their natal reef and do not cross deep water channels, resulting in detectible population genetic structure over short (< 50 km) distances (Gerlach et al.
2007). Adults are commonly found under overhangs during the day.
Pomacentrus coelestis produce benthic eggs and have a PLD of 18 – 20 days
(Gerlach et al.
2007). Late-stage P. coelestis larvae have a strong preference for oceanic waters ‘flavoured’ with reef odours and this may assist larvae in detecting reef habitat (Atema et al.
2002; Gerlach et al.
2007), although P. coelestis probably have the ability to cross deep channels of water (Gerlach et al.
2007). Adults congregate in channels at the reef edge. Previous genetic surveys have detected population structure at large spatial scales (i.e., between Taiwan and Japan, Liu et al.
2008) but not on small scales (< 50 km, between reefs, Gerlach et al.
2007).

Dascyllus trimaculatus produce benthic eggs and have a PLD of 22 – 26 days
(Wellington and Victor 1989), and nothing specific has been published about their larval habits. Adults are found on anemones or coral heads. Genetic surveys of mtDNA and microsatellites have shown strong differentiation between populations in the Indian (far western locations and Cocos-Keeling Islands; no samples from western
Australia) and Pacific Oceans and cryptic species groups within the central Pacific
(Bernardi et al.
2002; Leray et al.
2010).
Finally, Acanthurus triostegus produce pelagic eggs and have an average PLD of about 42 to 53 days (McCormick 1999; Juncker et al. 2006) but can delay metamorphosis associated with settlement (McCormick 1999). A. triostegus larvae are strong swimmers (Leis and Carson-Ewart 2001). Adults are fairly general in habit and move in large schools across the sand-reef interface (pers. obs.). Allozyme surveys have revealed significant population structure among regions within the Pacific Ocean
(Planes and Fauvelot 2002) and even at short distances (~200 km, Planes 1993;
Planes et al.
1998).

Literature Cited:
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Supplementary Figure: Maximum likelihood tree (GTR + G + I) of Apogon .
Bayesian posterior probabilities of branch support are given above branches and bootstrap support from a neighbor-joining are below branches (both measures of branch support reported as percentages with only values above 90% indicated).