A study of the population genetics of the prawn Penaeus monodon in northern and eastern Australian waters. Variations in gene frequencies of allozymes and common proteins (GPI,LGG,LT-1,MDH-1,MDH-2,MPI,PGDH,PGM) were used to estimate connectivity and dispersal between populations which range through locations in Western Australia, Northern Territory, Queensland and New South Wales. Statistical analyses and clustering procedures were carried out.Collection of samples were from 7 locations throughout the species range in Australia: Clarence River, Townsville, Cairns, Weipa, Melville Island, Joseph Bonaparte Gulf, De Grey River.A later study was conducted on South Afican samples, see separate metadata record. To estimate connectivity and dispersal between Penaeus monodon populations in northern and eastern Australia. First systematic survey of genetic variation of P. monodon populations over a wide geographic range. Highly significant differences between western and the northern and eastern populations were demonstrated.

This record is derived from DEC Marine Policy Branch Endnote library and spatially referenced SIER Database.

A study of the population genetics of giant clams of the genus Tridacna from the Great Barrier Reef and the West Pacific. Variations in gene frequencies of allozymes and common proteins were used to estimate connectivity and dispersal between populations, and to determine the phylogeny of the genus (discrete species identities). Species studied were Hippopus hippopus, Hippopus porcellanus, Tridacna crocea, Tridacna derasa, Tridacna gigas, Tridacna maxima, Tridacna squamosa and Tridacna tevora. Not all loci were examined for all species.Allele frequencies at 6 polymorphic loci of 860 individual clams sampled from 19 populations of Tridacna maxima throughout the Pacific between November 1989 and October 1991 were examined. Collection locations were: Myrmidon, Davies, Michaelmas, Thetford, 13125, 21200, 20396 and Stapleton Reefs on the Great Barrier Reef; Marovo and Nggela in the Solomon Islands; Mili in the Marshall Islands; Bantayan and Tawi-tawi in the Philippines; Te puka in Tuvalu; Abiang and Abemana in Kiribati; Makogai and Makodragi in Fiji; and Aitutaki in the Cook Islands. Loci were: LDH-1, MDH-2, PGM-2, DIA, LGG-1, GSR.Seven polymorphic loci (GPI, MDH-1, PGM, DIAPH, AK, LGG-1, LGG-2) from 159 individuals of T. gigas were sampled from 7 populations thoughout the West Pacific (Marovo, Russell, Isabel and Nggela in the Solomon Islands; Silliman in the Philippines; Abemana in Kiribati; and Mili in the Marshall Islands) and compared to data previously obtained in 1990 from 393 individuals from 6 populations (Myrmidon, Grub, Michaelmas, Thetford, 13125 and Stapleton Reefs) from the Great Barrier Reef.28-40 individuals from 14 populations of Tridacna derasa were sampled from sites on the Great Barrier Reef (2 sites from each of Myrmidon, Bowl, 13125, 21200, 20396; and one site from Michaelmas and Escape Reefs), and from one site each in the Philippines (Scarborough Shoals) and Fiji (Makogai). Gene frequencies at 9 polymorphic loci (GPI, LDH-1, MDH-1, MDH-2, PGM, DIAPH, LGG-1, ENOL, GSR)were examined.Gene frequencies at 26 loci for 8 species of giant clam were examined. Samples were obtained between November 1989 and October 1991. Source and number of individuals sampled was: Hippopus porcellanus (Philippines, 3); Hippopus hippopus (3 -Great Barrier Reef); Tridacna squamosa (8 - GBR, Fiji, Solomon Islands); Tridacna crocea (6 - GBR, Solomon Islands); Tridacna maxima (9 - GBR, Solomon Islands, Cook Islands); Tridacna gigas (9 - GBR, Solomon Islands, Kiribati); Tridacna derasa (9 - GBR, Fiji, Palau); Tridacna tevora (1- Fiji). Polymorphic loci examined were: AAT-1, AK-1, AK-2, DIA-1, ENO-1, EST-1, GPI-1, GSR-1, IDH-1, LDH-1, LDH-2, LGG-1, LGG-2, LP-1, LP-2, LP-3, MDH-1, MDH-2, ME-1, MPI-1, NDH-1, NDH-2, PGK-1, PGM-1, PGM-2. To estimate connectivity and dispersal between Tridacna populations, and to determine the discrete species identities.

A study of the population genetics of squid of the genus Loligo was carried out at 9 northern Australian locations. Variations in gene frequencies of allozymes and common proteins were used to estimate connectivity and dispersal between populations, and to determine the phylogeny of the genus (discrete species identities). Two previously described species (Photololigo chinensis, P. edulis) were discovered to actually be four species.Sampling locations were: Northwest Shelf, Timor Sea, Arafura Sea, Gulf of Carpentaria, Torres Strait, Cape York, Princess Charlotte Bay, Townsville, Brisbane. Sample sizes for the locations ranged between 19 and 447 individuals. Species identified were: Photololigo chinensis, sp.1, sp.2, sp.3.Following preliminary scoring for 76 enzymes, 9 enzymes were selected for routine scoring of genotypes: ACON, AK, ENOL, IDH, MDH-3, MPI, PGDH, PGM, G3PDH. To estimate connectivity and dispersal between populations, and to determine the phylogeny of discrete species.

Population genetic structure was studied in one nearshore (Great Palm Island) and two offshore (Rib Reef and Reef 18-026) populations of Stichopus chloronotus on the Great Barrier Reef. Two stations approximately 500m were sampled on each reef at depths between 1 and 2 m. At each station, 30-40 individuals were sampled within a radius of 30m, in early November 1996. The sampling time in November was chosen to increase the likelihood of finding mature gonads in the sampled animals.Genetic variation at 5 polymorphic loci was examined using allozyme electrophoresis. The polymorphic enzymes examined were: hexokinase (E.C. 2.7.1.1; HK), mannose- 6-phosphate isomerase (E.C. 5.3.1.8; MPI), phosphoglucomutase (E.C. 5.4.2.2; PGM), triose-phosphate isomerase (E.C. 5.3.1.1; ¹PI) and peptidase using valylleucine as substrate (E.C. 3.4.11/13; Estimates of the level of asexual reproduction were made using the ratios of the number of sexually produced individuals to sample size, observed genotypic diversity (Go) to expected genotypic diversity (Ge), and number of genotypes (Ngo) to sample size. Values of Go/Ge much smaller than one indicate the occurrence of clonal reproduction.F-statistics were used to partition genetic variation into that occurring within populations (FIS) and that occurring between populations (FST). To study levels of asexual reproduction and genetic variations occurring within and between populations. Stichopus chloronotus is a common holothurian species on Indo-Pacific coral reefs.

A study of the population genetics of the starfish Linckia laevigata throughout the Indian and Pacific Oceans. Seven allozyme loci (GPI, ENO, HK, LP, LT-1, LT-2, SOD) were examined. Variations in gene frequencies of allozymes and common proteins, as well as mitochondrial D-loop DNA (the Restriction Fragment Length Polymorphism - RFLP) were used to estimate connectivity and dispersal between populations in the region. Genetic differentiation of populations within and among oceans.To determine whether colour morphs were genetically differentiated. 1020 individuals were sampled from 2 sites from each of 10 collection locations (Escape, Evening, Davies, Grub, Lodestone, Holbourne, Tern, Sanctuary, 22112, Sykes) between July 1991 and March 1992.608 individuals were added to the previous set (analyses included all samples). These were collected from 18 localities: Australia (Western Australia - Mermaid, Clerke, Imperieuse, Scott and Serangapatum Reefs - Torres Strait, Burke Reef); Fiji (Dravuni, Suva); Guam (Asan, Luminao); Japan (Sesoko, Okinawa); New Caledonia; Philippines (Bolinao, Dumaguete); Solomon Islands (Gizo, Guadacanal).92 individuals were collected from Thailand (Kuta Beach, Phuket Marine Station, Waeo Island) and South Africa (7 reefs in the St. Lucia and Maputuland Marine Reserves); analyses included previously collected data. These samples were of the orange colour morph and were compared the previous data in which the royal blue morph is predominant.

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 27:1-47Basic 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. The aim of the study was to investigate gene flow between populations separated by different geographic scales (~20-2000 km), along the north-east coast of Australia, Torres Strait and the Solomon Islands, to provide information on connectivity to assist management and add to fundamental knowledge on the biology of this ecologically and economically important species.

The aims of this study for the WAMSI Dredging Science Program were: To establish fundamental knowledge on the genetic diversity of seagrass meadows; and if this varies among sites and with different environmental conditions, particularly clear and turbid water; To understand the gene flow among populations; and To inform the design of mesocosm and laboratory experiments on seagrass resilience. This study was the first of its kind to examine the patterns of genetic diversity in seagrasses in the Pilbara region of WA. Three species were assessed: Halophila ovalis (6 populations), Halodule uninervis (8 populations) and Thalassia hemprichii (3 populations) at a range of spatial scales, within a meadow (centimetres−metres), among meadows at a local scale (2−60 km) and among meadows at a regional scale (up to 500 km). Due to the varied distribution of species we could not sample all species across the same spatial scale and range of environments, so we designed a nested approach, with sites replicated at a distance of 2−5 km, and then different species at varied larger spatial scales.

The distribution of genetic variation of 7 microsatellite DNA markers in the mass-spawning coral Acropora tenuis was measured to infer patterns of connectivity among reef systems in the offshore (Scott Reef and Rowley Shoals) and coastal (Dampier Archipelago and Ningaloo Reef) zones of northwest Australia.Samples from 1156 colonies of Acropora tenuis were collected from 6 or 7 sites (more than 40 colonies were collected from most sites) at each of the Scott Reef, Rowley Shoals, Ningaloo Reef and the Dampier Archipelago systems.To minimize multiple collections of the same genet that may have been produced through asexual fragmentation or propagation (ramets), only a colony that was physically distinct and more than 1.5 m from other colonies was sampled. Note this provided an unbiased underestimate of the real contribution of asexual reproduction. Clonality was measured by calculating the proportion of unique multilocus genotypes as (Ng:N) at each site: of the 1156 samples collected, 1061 had unique multilocus genotypes.To explore the historical genetic connections among sites and systems, the amount of genetic variation were analysed within and among sites with respect to different alleles (FST), and on the sum of squared size differences of the alleles, assuming a stepwise model of mutation (RST).To further quantify the relationships among sites, 3 genetic distance measures between pairs of sites were calculated: DLR, which compares the likelihoods of complete multilocus genotypes in two populations; DS, Nei's standard genetic distance; and pairwise FST.Genetic diversity measures were calculated with FSTAT v2.9.3 as an unbiased estimate of gene diversity (HSK) and allelic richness (RS) per locus and site. The loci names use a prefix for the species followed by 2 or 5 according to the repeat motif type (di- or pentamer), followed by a number: Amil2-006, Amil2-010, Amil2-011, Amil2-012, Amil2-018, Amil2-022, Amil5-028. To assess genetic structure and diversity using 7 DNA microsatellite loci of the mass-spawning hard coral, Acropora tenuis, from a series of isolated and discontinuous coastal and offshore reef systems in northwest Australia.To test whether genetic and genotypic (clonal) diversities vary between the high-latitude, offshore reefs and the low latitude, coastal reefs.To gain further insight into degree of isolation, effective population size and the importance of asexual versus sexual reproduction.

This record is derived from DEC Marine Policy Branch Endnote library and spatially referenced SIER Database. KEYWORDS: Genetics/Fauna/Turtle/Population