The Great Barrier Reef (GBR) is a continental archipelagic system of 5
000 reefs and shoals stretching >2000 km along the east Australia coas
t. The interconnectivity of these reefs should determine the choice of
biological management units, which for most biota will reflect the di
spersal of their eggs and/or larvae. A comparative approach using popu
lation genetics was used to ask whether the along-shore dispersal of c
oral reef fishes is influenced by the duration of this mobile phase. S
even species of coral reef fish, selected from three families to provi
de a range of taxonomic diversity and pelagic larval durations, were t
ested for genetic homogeneity between two regions of the GBR separated
by 1000 km. A spectrum of potential dispersal capabilities was analyz
ed from that of Acanthochromis polyacanthus, a damselfish with brood c
are that uniquely lacks pelagic larvae, to that of Ctenochaetus striat
us, a surgeonfish with large, specialized larvae that spend several mo
nths in the plankton. A total of 19 enzyme systems and general protein
s were examined from multiple populations in each region to provide a
base of 32 loci for these comparisons. With one exception, species sam
pled from different coral reefs within regions showed statistically si
gnificant heterogeneities across multiple loci, indicative of chaotic
genetic patchiness among the samples. The exception was an anemonefish
, Amphiprion melanopus, that had to be collected from large areas on e
ach reef because of its law densities. The homogeneity of allele frequ
encies at local scales for this species suggests that the genetic patc
hiness observed in others may be a within-reef phenomenon that was man
ifested at the reef scale by our pseudoreplicated sampling strategy. A
fter pooling local variability, all but two species showed significant
regional differences. The exceptions were the pair (Ctenochaetus stri
atus, Pterocaesio chrysozona) with the longest larval durations. Acant
hochromis polyacanthus showed increased variation at this larger scale
, consistent with a major stock division between the two regions. The
logarithm of genetic Variation between northern and southern populatio
ns (measured by Weir and Cockerham's F-st) was correlated with mean la
rval duration by an inverse linear relationship that explained 85% of
the variance in the global data set. Comparison with an outgroup (Amph
iprion melanopus from the Chesterfield Reefs, 1000 km east in the Cora
l Sea) confirmed the genetic cohesion of mainland populations for the
species with shortest larval duration and shows that our empirical rel
ationship applies only within the context of the highly connected GBR.
On this basis, calculations of gene flow (N(e)m, the number of effect
ive migrants per generation) between geographic regions predict panmix
is for species with larval durations exceeding I mo. Many common speci
es have shorter dispersal times, from which classical ''isolation-by-d
istance'' models predict differentiation between northern and southern
populations at genetic equilibrium. Given that modern populations on
the GBR are <10 000 yr old, however, there has not been sufficient tim
e for such differences to evolve in situ and we consider alternative s
cenarios for the observed heterogeneities. Comparisons with invertebra
te taxa sampled over the same spatial scales imply lower gene flows in
fish despite longer pelagic durations. This suggests that fish larvae
may use their greater mobility to retard, rather than enhance, disper
sal due to hydrodynamic advection.