Irma S. Arlyza

Isolation and characterization of twenty-four polymorphic microsatellite loci for the topical seagrass, Thalassia hemprichii

Twenty-four polymorphic microsatellite loci were developed for the tropical seagrass, Thalassia hemprichii. Microsatellite enriched genomic libraries were constructed and subsequently sequenced using Pacific Biosciences SMRT technology. The 24 loci were characterized in 19 individuals from the Tukang Besi Islands, South East Sulawesi, Indonesia. Observed levels of heterozygosity ranged from 0.26 to 0.95 with a mean of 4.7 alleles per locus. No pairs of loci showed evidence of significant linkage disequilibrium and one locus significantly deviated from Hardy–Weinberg expectations.

Isolation and characterization of eighteen polymorphic microsatellite loci for the topical seagrass, Syringodium isoetifolium

Eighteen polymorphic microsatellite loci were developed for the tropical seagrass, Syringodium isoetifolium. Microsatellite enriched genomic libraries were constructed and subsequently sequenced using Pacific Biosciences SMRT technology. The 18 loci were characterized in 24 individuals from the Indonesian archipelago. Observed levels of heterozygosity ranged from 0.14 to 0.91 with a mean of 3.7 alleles per locus. Four pairs of loci showed evidence of significant linkage disequilibrium and one locus deviated significantly from Hardy–Weinberg expectations.

Eighteen microsatellite loci for the crown-of-thorns starfish, Acanthaster planci

Eighteen polymorphic microsatellite loci were developed for the crown-of-thorns starfish, Acanthaster planci, using 454 sequencing of microsatellite enriched genomic libraries. The 18 loci were characterized in 25 individuals from the Indonesian archipelago. We found a mean of 5.9 alleles per locus and observed levels of heterozygosity ranged from 0.120 to 0.958. Three loci significantly deviated from Hardy–Weinberg expectations and no pairs of loci showed significant evidence of linkage disequilibrium.

Isolation and characterization of twenty-one polymorphic microsatellite loci for Polycarpa aurata using third generation sequencing

Twenty-one microsatellite loci were developed for the tropical ascidian, Polycarpa aurata. Microsatellite enriched genomic libraries were constructed and sequenced using Pacific Biosciences single molecule real time sequencing technology. The 21 loci were characterized in 20 individuals from Alor, Indonesia. Observed levels of heterozygosity ranged from 0.30 to 1.00 with a mean of 8.2 alleles per locus. Loci PA21 and PA45 showed evidence of significant linkage disequilibrium and three loci significantly deviated from Hardy–Weinberg expectations.

Development of 15 microsatellite loci for Protoreaster nodosus (Echinodermata; Asteroidea)

Fifteen polymorphic microsatellite loci were developed for the horned sea star, Protoreaster nodosus, using 454 sequencing of microsatellite enriched genomic libraries. The 15 loci were characterized in 24 individuals from the Indonesian archipelago. We found a mean of 7 alleles per locus and observed levels of heterozygosity ranged from 0.042 to 0.875. All loci confirmed to Hardy–Weinberg expectations and no pairs of loci showed significant evidence of linkage disequilibrium.

Diagnostic description and geographic distribution of four new cryptic species of the blue-spotted maskray species complex (Myliobatoidei: Dasyatidae; Neotrygon spp.) based on DNA sequences

Nine morphologically similar but genetically distinct lineages in the blue-spotted maskray species complex, previously Neotrygon kuhlii (Müller and Henle) qualify as cryptic species. Four of these lineages have been previously described as Neotrygon australiae Last, White and Séret, Neotrygon caeruleopunctata Last, White and Séret, Neotrygon orientale Last, White and Séret, and Neotrygon varidens (Garman), but the morphological characters used in the descriptions offered poor diagnoses and their geographic distributions were not delineated precisely. The objective of the present work is to complete the description of the cryptic species in the complex. Here, an additional four lineages are described as new species on the basis of their mitochondrial DNA sequences: Neotrygon bobwardi, whose distribution extends from the northern tip of Aceh to the western coast of Sumatera; Neotrygon malaccensis, sampled from the eastern part of the Andaman Sea and from the Malacca Strait; Neotrygon moluccensis, from the eastern half of the Banda Sea; and Neotrygon westpapuensis from the central portion of northern West Papua. The geographic distributions of N. australiae, N. coeruleopunctata, N. orientale, and N. varidens are updated. For each species, a diagnosis is provided in the form of a combination of private or partly-private nucleotides at 2–4 nucleotide sites along a 519-base pair fragment of the CO1 gene. We believe that the present taxonomic revision will provide information relevant to the sound management and conservation of cryptic species of the blue-spotted maskray in the Coral Triangle region.

Population genetic subdivision of seagrasses, Syringodium isoetifolium and Thalassia hemprichii, in the Indonesian Archipelago

Abstract The population genetics of two seagrasses, Syringodium isoetifolium and Thalassia hemprichii were assessed throughout the Indonesian Archipelago. We genotyped 257 blades of S. isoetifolium at 15 microsatellite loci collected from 14 sampling sites and 406 blades of T. hemprichii at 17 microsatellite loci from 16 sampling sites. Once clones were removed, 165 individuals of S. isoetifolium and 389 of T. hemprichii were used in downstream analyses. Bayesian clustering methods revealed two genetically distinguishable clusters in each species, although the geographic boundaries of these clusters differed. Syringodium isoetifolium has a cluster that is located exclusively on the shallow Sunda Shelf and appears to follow the demarcation defined by Wallace’s line. Thalassia hemprichii, however, has a genetically distinguishable cluster located within the Banda Sea. The Banda Sea has unique physical oceanographic conditions, which may be driving the observed differentiation in T. hemprichii. We speculate that historical sea level changes exposing the Sunda Shelf, and the unique oceanographic conditions of the Banda Sea are contributing to the observed population differentiation. The observed genetic differentiation in both species is a possible starting point for speciation.

Isolation and characterization of nineteen microsatellite loci for the collector sea urchin, Tripneustes gratilla

Nineteen polymorphic microsatellite loci were developed for the collector sea urchin, Tripneustes gratilla. Microsatellite enriched genomic libraries were constructed and subsequently sequenced using Roche 454 technology. The 19 loci were characterized in 24 individuals from the Indonesian archipelago. Observed levels of heterozygosity ranged from 0.21–0.92 with a mean of 12.2 alleles per locus. No pairs of loci showed evidence of significant linkage disequilibrium and 5 loci significantly deviated from Hardy–Weinberg expectations.

Analysis of Space Suitability Based on Marine Agriculture in The Small Islands Around Makassar

The purpose of research is to analyze the suitability of the waters and environmental carrying capacity for utilization of marine aquaculture. Analysis of the data using conformity matrix is based on the physical-chemical parameters of the waters. Analysis of environmental carrying capacity performed to estimate the number of units that can be supported on the cultivation potential areas. The analysis is done by desk study approach, surveys and direct measurements. The analysis showed: (a) the condition of the waters of small islands around Makassar suitable for utilization of aquaculture, and (b) The water potential for seaweed cultivation around 110,012.6 ha, and the effective area about 243.225 ha. Broad potential area for grouper aquaculture by floating net system is approximately 1961.3 ha, and an effective area approximately about 209.97 ha. The results of this analysis are expected to be useful as: (1) a material consideration in the formulation of investment policy and research, (2) a reference for the public and private sectors in developing of sustainable aquaculture system effort.

Isolation and characterization of twenty-three polymorphic microsatellite loci for Linckia laevigata

Twenty-three polymorphic microsatellite loci were developed for the tropical sea star, Linckia laevigata. Microsatellite enriched genomic libraries were constructed and subsequently sequenced using Roche 454 technology. The 23 loci were characterized in 21 individuals from Pulau Derawan, Indonesia. Observed levels of heterozygosity ranged from 0.20 to 1.00 with a mean of 8.0 alleles per locus. No pairs of loci showed evidence of significant linkage disequilibrium and 4 loci significantly deviated from Hardy–Weinberg expectations.