Jennifer R. Ovenden

NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data.

NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single‐sample estimators (updated versions of the linkage disequilibrium and heterozygote‐excess methods, and a new method based on molecular coancestry), as well as the two‐sample (moment‐based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross‐method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

A review of the application of molecular genetics for fisheries management and conservation of sharks and rays

Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.

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.

Mitochondrial DNA analyses of the red rock lobsterJasus edwardsii supports an apparent absence of population subdivision throughout Australasia

Nucleotide sequence polymorphism in the mitochondrial genomes of 132 adult lobsters (Jasus edwardsil) collected from widespread locales across southern Australia and from New Zealand (April 1989 to June 1990) was assayed, using six restriction endonucleases, to test the hypothesis of a lack of genetic subdivision in a marine species with a long-lived planktonic larva. The mean amount of mtDNA diversity among the 132 mitochondrial genomes was 0.77%. Phenetic clustering and gene-diversity analyses, as well as pairwise comparison of the genetics of specimens from each, or grouped, locales did not detect the presence of genetic subdivision across approx 4600 km of Southern Ocean habitats. The inability of this study to detect population subdivision does not preclude fortutitous, active or habitat-specific larval settlement from producing and maintaining hidden groupings. If genetic homogeneity is maintained in this species by larval dispersal in ocean currents flowing to the east, then westerly populations may deserve special conservation status.

IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo‐West Pacific

The Indo‐West Pacific (IWP), from South Africa in the western Indian Ocean to the western Pacific Ocean, contains some of the most biologically diverse marine habitats on earth, including the greatest biodiversity of chondrichthyan fishes. The region encompasses various densities of human habitation leading to contrasts in the levels of exploitation experienced by chondrichthyans, which are targeted for local consumption and export. The demersal chondrichthyan, the zebra shark, Stegostoma fasciatum, is endemic to the IWP and has two current regional International Union for the Conservation of Nature (IUCN) Red List classifications that reflect differing levels of exploitation: ‘Least Concern’ and ‘Vulnerable’. In this study, we employed mitochondrial ND4 sequence data and 13 microsatellite loci to investigate the population genetic structure of 180 zebra sharks from 13 locations throughout the IWP to test the concordance of IUCN zones with demographic units that have conservation value. Mitochondrial and microsatellite data sets from samples collected throughout northern Australia and Southeast Asia concord with the regional IUCN classifications. However, we found evidence of genetic subdivision within these regions, including subdivision between locations connected by habitat suitable for migration. Furthermore, parametric FST analyses and Bayesian clustering analyses indicated that the primary genetic break within the IWP is not represented by the IUCN classifications but rather is congruent with the Indonesian throughflow current. Our findings indicate that recruitment to areas of high exploitation from nearby healthy populations in zebra sharks is likely to be minimal, and that severe localized depletions are predicted to occur in zebra shark populations throughout the IWP region.

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.

Evidence for reproductive philopatry in the bull shark Carcharhinus leucas

Reproductive philopatry in bull sharks Carcharhinus leucas was investigated by comparing mitochondrial (NADH dehydrogenase subunit 4, 797 base pairs and control region genes 837 base pairs) and nuclear (three microsatellite loci) DNA of juveniles sampled from 13 river systems across northern Australia. High mitochondrial and low microsatellite genetic diversity among juveniles sampled from different rivers (mitochondrial φ(ST) = 0·0767, P < 0·05; microsatellite F(ST) = -0·0022, P > 0·05) supported female reproductive philopatry. Genetic structure was not further influenced by geographic distance (P > 0·05) or long-shore barriers to movement (P > 0·05). Additionally, results suggest that C. leucas in northern Australia has a long-term effective population size of 11 000-13 000 females and has undergone population bottlenecks and expansions that coincide with the timing of the last ice-ages.

Spatial genetic subdivision between northern Australian and southeast Asian populations of Pristipomoides multidens: a tropical marine reef fish species

Nucleotide sequence polymorphism in the left domain of the control region of the mitochondrial genome of over 700 goldband snapper (Pristipomoides multidens) was surveyed using both direct sequencing and innovative restriction enzyme cleavage analysis techniques. Southeast Asian populations were sampled adjacent to western Irian Jaya, northern Papua New Guinea and western Timor. Six Australian populations were sampled from adjacent to Exmouth in western Australia to Weipa in the northern Gulf of Carpentaria. The results show that significant genetic structure occurs among Indonesian and Australian waters along national boundaries; 14% of the total molecular variance among restriction site haplotypes was due to genetic distinction between Indonesian and Australian samples. Several lines of evidence suggest that gene flow does not occur freely along the northern and western Australian coastline, particularly on the northwestern Kimberley coast. Australian fisheries managers need to be alerted to the possibility of at least one genetically distinct population of this important commercial species which should be protected from over-harvesting that may otherwise lead to localised extinction and the erosion of genetic diversity. There is no convincing biological argument for the observed genetic disjunction in the Kimberley area. It may be due to the combined effect of past sea-level changes, sampling error or patterns of exploitation. # 2002 Elsevier Science B.V. All rights reserved.

POPULATION-GENETIC STRUCTURE OF A PHILOPATRIC, COLONIALLY NESTING SEABIRD, THE SHORT-TAILED SHEARWATER (PUFFINUS TENUIROSTRIS)

Short-tailed Shearwaters (Puffinus tenuirostris) are a numerous, colonially nest- ing seabird that is strongly philopatric. We applied restriction-enzyme analysis of mito- chondrial DNA (mtDNA) to 335 individuals from 11 colonies across southeastern Australia to assess population-genetic structure and the amount of genetic variability in this species. Eleven 6/ 5.33-base and four 4-base restriction enzymes revealed 25 and 48 mtDNA haplotypes in two overlapping surveys of 215 individuals from seven colonies and 231 individuals from eight colonies, respectively. A low mean sequence diversity among individuals (0.247%) and lack of spatial structuring of mtDNA haplotypes suggest a lack of population-genetic structure and a reduced ancestral population size during glaciation, followed by a population and range expansion. Intracolony mtDNA diversities in three recently established colonies and in one colony that has experienced a recent bottleneck were comparable to mtDNA diversities within larger and older colonies. This suggests that, despite strict philopatry in those colonies, colony founding and recovery from population reduction occurs via immigration of a large number of individuals. Received 27 April 1993, accepted 11 November 1993.

Evidence of stock separation in southern hemisphere organge roughy (Hoplostethus atlanticus, Trachichthyidae) from restriction-enzyme analysis of mitochondrial DNA

Restriction enzyme analysis of mitochondrial DNA (mtDNA) was used to test for genetic homogeneity of orange roughy (Hoplostethus atlanticus) in the southern hemisphere. Two hundred and eighty-six orange roughy specimens were collected from seven general localities: the Great Australian Bight; South Australia (off southeastern Kangaroo Island); the west coast of Tasmania; the east coast of Tasmania; New South Wales; New Zealand and South Africa. Mitochondrial DNA was extracted from developing ovary tissue and analysed with 10 six-base enzymes and 3 four-base enzymes. Both forms of analysis revealed a low level of genetic diversity in this species. The six-base enzyme study found no evidence of reproductively isolated populations of orange roughy in southeastern Australian waters. However, an analysis of 107 fish with 3 four-base enzymes identified at least partial genetic separation of the New South Wales (NSW) sample of orange roughy from South Australian (off southeastern Kangaroo Island) and Tasmanian samples. This finding supports biological evidence for the presence of a distinct subpopulation of orange roughy in NSW waters. The four-base study also provided evidence of the presence of genetically distinct samples of orange roughy occurring in the same localities off southeastern Kangaroo Island from consecutive years. Additional sampling and the use of a greater number of four-base enzymes may be needed to determine if any genetic structuring exists among orange roughy south of New South Wales.