Raewyn Street

The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus).

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long‐term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments‐based and maximum‐likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long‐term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non‐infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.

Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle

The East Indies triangle, bordered by the Phillipines, Malay Peninsula and New Guinea, has a high level of tropical marine species biodiversity. Pristipomoides multidens is a large, long‐lived, fecund snapper species that is distributed throughout the East Indies and Indo‐Pacific. Samples were analysed from central and eastern Indonesia and northern Australia to test for genetic discontinuities in population structure. Fish (n = 377) were collected from the Indonesian islands of Bali, Sumbawa, Flores, West Timor, Tanimbar and Tual along with 131 fish from two northern Australian locations (Arafura and Timor Seas) from a previous study. Genetic variation in the control region of the mitochondrial genome was assayed using restriction fragment length polymorphism and direct sequencing. Haplotype diversity was high (0.67–0.82), as was intraspecific sequence divergence (range 0–5.8%). FST between pairs of populations ranged from 0 to 0.2753. Genetic subdivision was apparent on a small spatial scale; FST was 0.16 over 191 km (Bali/Sumbawa) and 0.17 over 491 km (Bali/Flores). Constraints to dispersal that contribute to, and maintain, the observed degree of genetic subdivision are experienced presumably by all life history stages of this tropical marine finfish. The constraints may include (1) little or no movement of eggs or larvae, (2) little or no home range or migratory movement of adults and (3) loss of larval cohorts due to transport of larvae away from suitable habitat by prevailing currents.

Genetic population structure of mangrove jack, Lutjanus argentimaculatus (Forsskål)

Translocations of mangrove jack, Lutjanus argentimaculatus (Forsskal 1775), to increase angling opportunities in artificial impoundments are foreshadowed in Queensland. To evaluate genetic population structure before translocations occur, mangrove jack were collected from three sites on the Queensland coast and from one site on the north-western coast of Western Australia. Allelic variation at four dinucleotide microsatellite loci was high: gene diversity (heterozygosity) ranged from 0.602 to 0.930 and allelic counts from 10 to 24. Genetic differentiation among collection sites was weak: estimates of FST were 0.002 for all four sites, and less (FST = 0.001) across a major biogeographical boundary (the Torres Strait region). Nucleotide sequence from two mitochondrial regions (control, 375 base pairs, and ATPase, 415 base pairs) was obtained from a subset of the Australian and additional Indo-Pacific (Indonesian and Samoan) mangrove jack. Haplotype diversity was high (control region, 33 haplotypes for 34 fish; ATPase region, 13 haplotypes for 56 fish). Phylogenetic analysis of mitochondrial DNA sequence data could not discern a relationship between tree topology and geography. These results suggest that mangrove jack in Queensland, and possibly throughout Australia, experience high levels of gene flow. The artificial gene flow caused by permitted translocations is unlikely to exceed natural levels. Fine-scale ecological matching between donor and recipient populations may increase stocking success, and is important if translocation is needed as a species recovery tool in the future.

Australian lungfish (Neoceratodus forsteri: Dipnoi) have low genetic variation at allozyme and mitochondrial DNA loci: a conservation alert?

Genetic variation at allozyme and mitochondrialDNA loci was investigated in the Australianlungfish, Neoceratodus forsteri Krefft1870. Tissue samples for genetic analysis weretaken non-lethally from 278 individualsrepresenting two spatially distinct endemicpopulations (Mary and Burnett rivers), as wellas one population thought to be derived from ananthropogenic translocation in the 1890s(Brisbane river). Two of 24 allozyme lociresolved from muscle tissue were polymorphic.Mitochondrial DNA nucleotide sequence diversityestimated across 2,235 base pairs in each of 40individuals ranged between 0.000423 and0.001470 per river. Low genetic variation atallozyme and mitochondrial loci could beattributed to population bottlenecks, possiblyinduced by Pleistocene aridity. Limited geneticdifferentiation was detected among rivers usingnuclear and mitochondrial markers suggestingthat admixture may have occurred between theendemic Mary and Burnett populations duringperiods of low sea level when the drainages mayhave converged before reaching the ocean.Genetic data was consistent with theexplanation that lungfish were introduced tothe Brisbane river from the Mary river. Furtherresearch using more variable genetic loci isneeded before the conservation status ofpopulations can be determined, particularly asanthropogenic demands on lungfish habitat areincreasing. In the interim we recommend amanagement strategy aimed at conservingexisting genetic variation within and betweenrivers.

A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis

Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species‐specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real‐time high‐resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species‐specific genetic mutations that result in PCR products with unique melt profiles. A real‐time HRM PCR species‐diagnostic assay (RT‐HRM‐PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing.

Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae)

Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies.