17 to 141 individuals were collected from 8 populations of the fished holothurian species Holothuria scabra (Echinodermata: Holothuroidea), from north-east Australia, the Torres Strait, and the Solomon Islands and investigated by allozyme electrophoresis of 7 polymorphic loci.
Two shallow populations of Holothuria scabra were sampled in the area of Hervey Bay (Urangan, Tin Can Bay) in south Queensland during June 1998. Individuals from a deeper population in Hervey Bay (18-20 m) were obtained during 3 trawl shots using commercial prawn-trawling equipment.
One intertidal population was sampled ca. 800 km north Upstart Bay in 1998. Data from these samples were used in a previous study investigating the relationship between 2 colour morphs and the gene flow between deep and shallow populations. This population was re-sampled in May 2000 to investigate whether gene frequencies and the small size of individuals (as found in 1998) were stable over time.
During August 1999, samples were obtained from 2 reefs in the Torres Strait at the northern end of the GBR (Warrior Reef, Dungeness Reef). Two locations in the Solomon Islands, Kohinggo Island (Solomon Island A) and Kolombangarra Island (Solomon Island B), were sampled in December 1999.
Samples from intertidal populations were taken during low tides by walking on the mud flats. During these periods, holothurians in shallow tide pools, usually with at least a sparse seagrass cover, migrate to the surface of the sediment. Since large areas had to be covered to obtain sufficient individuals, no effort was made to obtain subsamples within each of the populations. The length of all individuals was recorded to the nearest centimetre. A subsample of the gut lining (cleaned from sediments) was snap frozen in liquid nitrogen for later analyses.
Seven polymorphic enzyme loci were surveyed using allozyme electrophoresis: PGM, HK, GPI, MDH, PEP-1, PEP-2 and PEP-3. Full details of staining and electrophoresis methods are given in:
Ballment E, Uthicke S, Peplow L, Benzie JAH (1997) Techniques for enzyme electrophoretic analysis of the holothurians Holothuria atra and Stichopus chloronotus (Holothuroidea: Aspidochirotida). Aust Inst Mar Sci (AIMS) Tech Rep Ser 27:1-47
Basic analyses of genetic variability were carried out using programs in the BIOSYS-1. F-statistics, cluster analyses and tests of conformation to Hardy-Weinberg expectations were performed using the TFPGA package.
The contribution of asexual reproduction to each population was calculated as described in detail in:
Uthicke S, Benzie JAH, Ballment E (1998) Genetic structure of fissiparous populations of Holothuria (Halodeima) atra on the Great Barrier Reef. Mar Biol 132:141-151.
Deviations from Hardy-Weinberg equilibrium for each locus at each reef were tested by an exact-test, using the conventional Monte Carlo method with the default settings in TFPGA.
To test for evidence of isolation by distance, Mantel¿s tests were performed on transformed (log + 1) geographic distance (km) and Rogers' genetic distances. The significance of Mantel's normalised Z was tested by 10000 random permutations using NTSYS-PC software.
