A study of the population genetics of the prawn Penaeus monodon in northern and eastern Australian waters. Mitochondrial D-loop DNA (and Restriction Fragment Length Polymorphism - RFLP) 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 6 locations throughout the species range in Australia: Townsville, Cairns, Weipa, Melville Island, Joseph Bonaparte Gulf, De Grey River.Some comparison was made with Indonesian and South African samples, see separate metadata record.Microsatellite markers were used in a further study of genetic variation among the Australian populations above. To estimate connectivity and dispersal between Penaeus monodon populations in northern and eastern Australia.To compare results with genetic analyses using allozymes. Separate metadata records apply for data relating to the genetic analyses using allozymes of Penaeus monodon from Australian waters and South Africa.

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.

Populations of Ceriops tagal var. tagal and C. tagal var. australis were sampled from five sites in northern Queensland in 1987. Collections were made from Missionary Bay (April), Port Douglas (July), Lucinda (October) and Cardwell (October). Samples were collected five times between March and December from the same six trees of each variety at Cape Ferguson, to detect seasonal variation in enzyme phenotypes. C. decandra was also sampled from the Murray River, Lucinda and Cardwell. Branch tips with at least two pairs of fully expanded leaves were collected and the apical buds and their stipules were removed and stored in liquid nitrogen.Twenty-one enzymes were investigated (AAT, ACON, ACP, ALP, DIA, EST, GDH, G3PD, GPI, G6PD, HK, IDH, LAP, LDH, MDH, ME, PER, 6PGD, PGM, SKDH, TPI). Eleven enzymes were resolved adequately for all samples of the three taxa (AAT, EST, GDH, GPI, IDH, LAP, MDH, PER, 6PGD, PGM, SKDH). This research was undertaken to investigate the taxonomic status of the two varieties of the mangrove tree Ceriops tagal using enzyme electrophoresis.

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.

Within-region genetic heterogeneity of Holothuria scabra populations in New Caledonia was examined through allozyme electrophoresis. Five locations, each separated by 60-130 km, were selected along the coast of New Caledonia and 2 replicate sites (8-23 km apart) were chosen within 4 of these locations on the west coast of the island. Only one site was selected on the northeast coast. Between 14 and 34 adult Holothuria scabra were collected from each site. A short section of the upper intestine (5-10 cm), without sediments, was dissected from each animal and stored in liquid nitrogen until analysed. Holothuria scabra samples from Bali (n=90) and Knocker Bay, Australia (n=47), and existing data from the western Pacific: Solomon Islands; Torres Strait; and the Queensland Coast (Upstart Bay and Hervey Bay) were compared with the data from New Caledonia to investigate larval connectivity over a wider geographic scale. Seven polymorphic enzyme loci were surveyed using allozyme electrophoresis: GPI, HK, MDH, PEP-1, PEP-2, PEP-3 and PGM. Basic analyses of genetic variability (allele frequencies, number of polymorphic loci, heterozygosity) were carried out. The allelic richness for each population was calculated. F statistics were calculated and genetic distance analyses, cluster analyses and Mantel tests were performed. This research was undertaken to improve understanding of the genetic differentiation between stocks of Holothuria scabra at different spatial scales so that the release of cultured juveniles in restocking programs can be planned in a responsible way to preserve the genetic diversity of existing stocks. Sampling sites in New Caledonia: A=Baie de Sainte-Marie; B= Ilot Maître; C=Ouano; D=Ilots Kundogi; E=Plateau de Béco; F=Pointe Pindaï; G=Pouangué; H=Ouaco; I=Récif Thaavaam (Ilot Cocotier).

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.

Population genetic structure was studied in two nearshore (Fantome and Great Palm Islands) and two midshelf (Rib and 18-026) reef populations of Holothuria atra on the Great Barrier Reef. Two stations approximately 500 m apart were sampled on each reef (only 150 m apart at Fantome Island due to the limited area in which the species occurs). At each station, 30-40 adult individuals (generally > 50 g) were sampled within a radius of 30m from a marker buoy, in early November 1996. The sampling time in November was chosen to increase the likelihood of finding mature gonads in the sampled animals. Female gonads were dark red, male gonads were orange; several small gonads were examined microscopically to determine whether they were ovaries or testes. Several inidivduals had gonads which were either immature or not detectable, these were exluded from the male/female analyses but included in other analyses.Genetic variation at 5 polymorphic loci was examined using allozyme electrophoresis. The polymorphic enzymes examined were: GPI, HK, LP, PGD and PGM. Measures describing the genetic variables for females, males and unsexed individuals were: sample size per locus; number of alleles per locus; percentage of loci that were polymorphic; heterozygosity (observed=Ho, expected=He); genotypic diversity (observed=Go, expected=Ge, and the ratio of Go to Ge); sample size (Ni); number of genotypes ((observed=Ngo, expected=Nge).Calculation were made on: the number of sexually produced individuals (N); and the ratios of Ngo to Nge; Ni to Ngo; N to Ni.Average weight (g), for females, males and unsexed individuals were recorded; and sex ratios for all sexed individuals and estimated annual fission rates calculated.F-statistics were used to partition genetic variation into that occurring within populations (FIS) and that occurring between populations (FST) for males, females and total individuals for both original and clonal genotype frequencies.A dendrogram was created to show genetic relationships between the populations of the 8 sites using UPGMA cluster algorithm and Nei's unbiased genetic distance. To describe the genetic structures of Holothuria atra using allozyme electrophoresis to quantify the extent of asexual reproduction and to extimate the importance of sexual recruitment in this fissiparous holothurian.

Transects were established in tidal forests in a series of embayments, rivers and islands between the tip of Cape York and Hinchinbrook Island. The transects were distributed so as to attempt to reveal the entire spectrum of floristic character likely to be found between the full influence of the coastal sea, and upstream and landward limits of tidal range. The complete dataset comprised 1391 individual sites. Over 40 plant species are now known to occur in the mangrove communities of northeastern Australia, and 35 of these were encountered in this survey. Several taxa, which are not normally considered members of a mangrove flora are included because of their utility as indicators. This research was undertaken to develop a better understanding of the mangrove vegetation in Australia by exploring the utility of classificatory techniques in describing mangrove vegetation to provide an overview account of mangrove forest diversity in northeastern Australia. The data lists species occurrences along transects at various locations as well as, for a number of the sites, information on their topographic heights above specified datum levels.

This data set is comprised of 2 files consisting of field observations and water quality measurements relevant to a publication on the classification and population status of the WV Spring salamander, Gyrinophilius subterraneus.

A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilization, and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. In Canada, eelgrass is managed as a single phylogroup despite occurring across three oceans and a range of ocean temperatures and salinity gradients. Previous research has focused on applying relatively few markers to reveal population structure of eelgrass, whereas a whole genome approach is warranted to investigate cryptic structure among populations inhabiting different ocean basins and localized environmental conditions. We used a pooled whole-genome re-sequencing approach to characterize population structure, gene flow, and environmental associations of 23 eelgrass populations ranging from the Northeast United States, to Atlantic, subarctic, and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise FST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the subarctic, consistent with colonization of the Arctic and Atlantic oceans from the Pacific less than 300 kya. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are predicted to be more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should thus ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require additional mitigation measures given their potential susceptibility to a rapidly changing climate. Cite this data as: Jeffery, Nicholas et al. (2024). Data from: Variation in genomic vulnerability to climate change across temperate populations of eelgrass (Zostera marina) [Dataset]. Dryad. https://doi.org/10.5061/dryad.xpnvx0kp2