Population variation in the mitochondrial cytochrome b gene of the orange roughy Hoplostethus atlanticus and the hoki Macruronus novaezelandiae

To describe the genetic relationship among regional populations of two commercially valuable species of marine fish, the orange roughy Hoplostethus atlanticus and the hoki Macruronus novaezelandiae, the mitochondrial (mt) DNA haplotypes of 59 individuals were defined by direct sequencing of the cytochrome b gene. Samples of orange roughy were collected on four fishing grounds around New Zealand, one off the west coast of Tasmania and one near South Africa from 1990–1991. Samples from hoki were collected on three fishing grounds around New Zealand and one off Tasmania during the same period. An average of 252 nucleotides were sequenced from each of 32 orange roughy and an average of 372 nucleotides from each of 27 hoki. Sequence variation allowed the definition of 9 unique orange roughy haplotypes and 5 hoki haplotypes. Genetic variation, as measured by both average sequence divergence and haplotype diversity, was high in the orange roughy (nucleotide diversity=0.590%, haplotype diversity=0.782) and low in the hoki (nucleotide diversity=0.076%, haplotype diversity=0.279) relative to a similar survey of the Atlantic cod, Gadus morhua. Differences in haplotype frequencies of orange roughy from New Zealand, Tasmania and South Africa were not significant, and the most common haplotype was found in similar frequencies in these three geographically distant regions. Differences in haplotype frequencies between the New Zealand and Tasmanian samples of hoki were significant, suggesting restricted gene flow between these two regions. The contrasting patterns of low but regionally subdivided genetic variation in the hoki versus high but geographically undifferentiated genetic variation in the orange roughy may be attributed to the low fecundity, slow maturation and long lifespan of the orange roughy relative to the hoki.     

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.     

Morphometric and meristic comparison of orange roughy (Hoplostethus atlanticus: Trachichthyidae) from the Puysegur Bank and Lord Howe Rise,New Zealand,and its implications for stock structure

Significant morphological differences were found between orange roughy, Hoplostethus atlanticus, caught in 1993 on the Puysegur Bank and those caught on the Lord Howe Rise, New Zealand. A total of 17 separate body measurements and counts were taken from each fish. Treating the sexes separately, significant differences were found between sites when linear relations between eight particular body measures and standard length were compared. The eight measures indicating differences in shape were head length, snout length, orbit diameter, maxilla width, premaxilla length, caudal peduncle, gill raker count, and anal fin count. Discriminant functions were used to compare sites and sexes, and these permitted a >90% success rate in distinguishing fish from the two sites. A discriminant function could not be found which successfully separated two separate tows made on the Puysegur Bank, indicating that phenotypic differences do not vary as much within a site as they do between sites. All analyses made suggested that fish from the two different areas had different body shapes. Morphological differences, such as those found in the current investigation, could only arise if the fish populations from the two areas were relatively discrete. There may be some movement of fish between areas, quite possibly enough to bring about relative genetic homogeneity, but clearly there is insufficient to prevent the two populations from differing phenotypically. These differences suggest that morphometric analysis may be a useful tool for distinguishing New Zealand orange roughy stocks.     

DNA fingerprints of orange roughy,Hoplostethus atlanticus: a population comparison

Genetic variability among Hoplostethus atlanticus collected from two spawning grounds east and west of New Zealand was examined using DNA fingerprints as revealed by hybridization with three clonal probes: 33.15, M13 and 3HVR. The 33.15 and 3HVR fingerprints revealed a complex pattern of restriction fragments, apparently refecting a multi-locus system of highly variable minisatellite alleles similar to the pattern of alleles reported in other vertebrates. The M13 fingerprints revealed a distinct pattern of restriction fragments of high molecular weight, reflecting a single-locus system that overlapped with the family of minisatellite alleles observed in 33.15 fingerprints. In a sample of 12 orange roughy collected on a single regional spawning site, the average percent similarity of 33.15 fingerprints was 21.15% (SD=17.75), the average percent similarity of 3HVR fingerprints was 14.32% (SD=14.45) and the inferred average allelic frequency of the M13 single-locus system was 0.071. A comparison of 33.15 and M13 fingerprints from two distant spawning sites ground New Zealand revealed no obvious regional differences. The variability of orange roughy fingerprints was so great, however, that regional comparisons could not be considered conclusive indicators of genetic identity. Our results provide a preliminary assessment of the power and pitfalls of using DNA-level markers for the population analysis of marine fish.     

Between-area differences in age and length at first maturity of the orange roughy Hoplostethus atlanticus

Mean age and length at onset of maturity were estimated for orange roughy (Hoplostethus atlanticus) populations off New Zealand, Namibia, and Great Britain. Significant between-area differences were apparent in both these parameters. Implications of the between-area differences on stock structure of orange roughy in New Zealand waters are discussed. A proportional relationship between age at onset of maturity and modal size of fish in the mature population is demonstrated. This is consistent with later-maturing fish experiencing a longer period at a pre-maturity growth rate that is relatively faster than the rate of somatic growth after maturity. Received: 22 December 1997 / Accepted: 5 May 1998     

Low levels of global genetic differentiation and population expansion in the deep-sea teleost <Emphasis Type="Italic">Hoplostethus atlanticus</Emphasis> revealed by mitochondrial DNA sequences

The orange roughy Hoplostethus atlanticus is a well-known commercial species with a global distribution. There is no consensus about levels of connectivity among populations despite a range of techniques having been applied. We used cytochrome c oxidase subunit I (COI) and cytochrome b sequences to study genetic connectivity at a global scale. Pairwise Φ_ST analyses revealed a lack of significant differentiation among samples from New Zealand, Australia, Namibia, and Chile. However, low but significant differentiation (Φ_ST = 0.02–0.13, P < 0.05) was found between two Northeast Atlantic sites and all the other sites with COI. AMOVA and the haplotype genealogy confirmed these results. The prevalent lack of genetic differentiation is probably due to active adult dispersal under the stepping-stone model. Demographic analyses suggested the occurrence of two expansion events during the Pleistocene period.     

Patch study of mortality,growth and feeding of the larvae of the southern gadoid Macruronus novaezelandiae

A discrete dense patch of eggs and larvae of hoki (Macruronus novaezelandiae) within the hoki spawning grounds off Westland, New Zealand, was sampled to examine prey selectivity by larvae and to obtain estimates of larval mortality and growth. The patch was tracked using a free-drifting drogue, and surveys of the horizontal distribution of larvae before and after the patch study indicated that the drogue had successfully followed the patch. Modal analysis of the size-frequency distributions of hoki larvae revealed up to six cohorts within the patch at any one sampling time, and a growth rate of 0.21 mm standard length per day. The daily mortality coefficient for larvae within the patch was 0.19, although this is considered to be an overestimate. Differences in the mean length between cohorts suggest that hoki have a synchronised, diel spawning periodicity, and results of a simple cellular design model revealed that ten continuous days of spawning were required to yield the observed size structure of the hoki larvae population within the patch. Diet analysis of larvae in the patch showed that copepods of the genus Calocalanus are actively selected, and are especially important in the diet of early-stage larvae. Based on aspects of larval diet, morphology, and rates of mortality and growth, it is hypothesised that hoki larvae are adapted to a low-food environment, and that predation is likely to be more important as a source of mortality than starvation.     

Population structure and life history of orange roughy (Hoplostethus atlanticus) in the SW Pacific: inferences from otolith chemistry

We examined site differences in the elemental composition of the primordium and ontogenetic variability of Sr in otoliths of fish from Australia and New Zealand and, as an out-group, the North Atlantic. Differences among sites in primordium composition are slight, but significant for all five elements assayed (Sr, Pb, Cu, Zn and Hg), but principally reflect differences between the North Atlantic and SW Pacific specimens, do not replicate for independent samples in the SW Pacific and constitute a poor “natural tag” in roughy, with <25% of fish successfully assigned to source location. However, mean Sr weight-fractions at the primordium showed similar latitudinal variation across sites in Australia, New Zealand and the Tasman Sea, indicating both spatially structured populations and a common structuring process across the region. Comparisons of ontogenetic variability of Sr in otoliths from juveniles and young adults within and between sites in the SW Pacific strongly support the hypothesis that variability in this element is site-specific and environmentally sensitive, although the environmental factors involved are not obvious. The otolith analysis confirms previous suggestions that juvenile and adult Hoplostethus atlanticus are relatively sedentary, but also indicates that the population sub-structuring by age within sites is more complex and there are likely to be more spawning areas in Australian waters than previously thought. More broadly, although single point analysis of otolith composition at the primordium resolves a population structure in roughy, alone it is not precise enough to test hypotheses about the processes causing this structure. Ontogenetic variability in Sr provides better resolution of spatial structure, even in a relatively homogenous marine environment like the deep ocean, and also provides insight into behavioural and ecological factors. Ontogenetic analyses of Sr in otoliths are expensive to obtain, require more effort in specimen preparation than single point analyses, and are difficult to compare statistically, but the increased information they yield warrants their broader consideration in marine species.     

Transition zone in otoliths of orange roughy (Hoplostethus atlanticus) and its relationship to the onset of maturity

A transition zone in the otoliths of orange roughy (Hoplostethus atlanticus) is described where annulus width decreases markedly. For fish sampled at spawning time, the relationship between gonad stage and the presence or absence of a transition zone is consistent with the hypothesis that this zone marks the onset of maturity, if allowance is made for some error in gonad staging and identification of the zone. Another data set from a non-spawning area after the spawning season is not consistent with the hypothesis. However, these latter data are considered less reliable because of the small size of the fish in the sample and difficulties in determining, outside the spawning season, whether a fish has been reproductively active. This hypothesis was used to provide estimates of the median age (30 yr) and length (31 cm) at the onset of maturity for the Chatham Rise, New Zealand population. These estimates are unaffected by the biases associated with the usual ogive method of estimation. Received: 27 June 1997 / Accepted: 1 July 1997     

Allozyme and mitochondrial DNA variation in orange roughy,Hoplostethus atlanticus (Teleostei: Trachichthyidae): little differentiation between Australian and North Atlantic populations

Allozyme and mitochondrial DNA (mtDNA) genetic variation was compared in orange roughy (Hoplostethus atlanticus Collett) collected from waters off southern Australia and from waters about 22 000 km away in the North Atlantic west of Scotland. Samples were screened for 11 polymorphic allozyme loci and with 9 restriction enzymes. Significant heterogeneity between the two areas was detected for three allozyme loci (ADA ^*, CK ^* and GPI-1 ^*), and the overall G _ST (gene-diversity statistic) value of 1% was small but significant. Significant mtDNA haplotype heterogeneity was observed after ²- of haplotype frequencies but not after a G _ST analysis. Nucleotide sequence-diversity analysis showed very low net divergence (0.0023%) between the two samples. The Australian orange roughy had a lower allozyme heterozygosity and a lower mitochondrial DNA nucleon diversity than the North Atlantic sample. The very limited, although significant, allozyme and mitochondrial DNA heterogeneity between these areas suggests that there is some gene flow between these two populations. The species appears to be widespread, with its presence reported from the southern Pacific, southern Indian, and northern and southern Atlantic Oceans, and it is likely that gene flow between the antipodes is mediated by stepping-stone exchange between adjacent populations rather than by direct migration.     

Genetic population structure of southern bluefin tuna (Thunnus maccoyii )

Samples of southern bluefin tuna, Thunnus maccoyii (Castelnau), taken from off the coasts of South Africa, Western Australia, South Australia and Tasmania from 1992 to 1994 were analysed for six polymorphic allozyme loci (ADA ^*, GDA ^*, GPI-A ^*, MPI ^*, PGDH ^* and PGM-1 ^*, n = 595 to 733 per locus) and for mitochondrial DNA variants revealed by three restriction enzymes (Bam HI, Bcl I and Eco RI) detecting polymorphic cut sites (n = 555). No significant spatial heterogeneity was detected. There were no sex-related differences in allele or mtDNA haplotype frequencies. Juveniles (30 to 35 cm and 46 to 54 cm) from what are thought to be two temporally-separated spawning peaks showed no significant genetic differentiation. There were also no significant differences in allele or haplotype frequencies between fish smaller than 70 cm and those larger than 70 cm. These data are consistent with the null hypothesis of a single unit stock of southern bluefin tuna, with a single spawning area. This is located to the south of Java and off the north-west coast of Australia. Received: 28 August 1996 / Accepted: 30 September 1996     

Age determination of orange roughy,Hoplostethus atlanticus (Pisces: Trachichthyidae) using210Pb:226Ra disequilibria

Natural levels of²¹⁰Pb:²²⁶Ra in otoliths of orange roughy,Hoplostethus atlanticus, from south-east Australian waters, were measured to determine fish ages radiometrically. Up to maturity, radiometric age estimates were consistent with a single constant otolith growth rate. Radiometric ages for juveniles were comparable with, but greater than, those obtained in a recent, validated New Zealand study which employed counts of annuli on the surface of otoliths. Beyond maturity, radiometric ages were obtained by modelling with an otolith growth rate set at 45% of the juvenile rate. Radiometric ageing confirms that orange roughy is very slow-growing, with an age at maturity (32 cm standard length, SL) of ~ 32 yr, and is very long-lived, with fish 38 to 40 cm being 77 to 149 yr old. These results have important implications for the management of the fishery.     

Reproductive variability over a four-year period in the sea urchin Evechinus chloroticus (Echinoidea: Echinodermata) from differing habitats in New Zealand

 The endemic New Zealand echinoid, Evechinus chloroticus (Valenciennes), was sampled approximately monthly from September 1990 to October 1994 at three sites in Tory Channel, Marlborough Sounds, New Zealand. These channel sites (outer, mid and inner) were up to 20 km from the open ocean and differed in their shore type, exposure to wave action and macrophyte abundance. E. chloroticus showed an annual reproductive cycle at each site, with gametogenesis commencing in the late austral winter and spawning in summer. Maximum gonad indices (reproductive potential) varied spatially, with the outer site generally having higher maximum gonad indices than the inner site, and temporally, with maximum gonad indices occurring earlier in 3 of the 4 seasons at the outer site than the inner site. The mid and inner sites showed much greater variation in maximum gonad indices (range 15.83 to 26.99% and 11.87 to 20.90%, respectively) than the outer site (range 19.31 to 22.95%). Reproductive output (weight of gametes released per gram echinoid) also varied, with the different sites showing significantly different outputs in the different years. A regression of maximum reproductive potential against reproductive output was significant ( p < 0.001), and had a positive slope with an r ² of 0.79. While, the initiation of gametogenesis was relatively synchronous between sites and years, and is possibly cued by increasing daylength, it progressed at different rates among populations. Spawning did show spatial and temporal variability, occurring near the time of highest sea-surface temperatures (∼15 °C). The observed variations in reproductive cycle may be related to small-scale variability in diet and environmental conditions. Furthermore, asynchronous spawning, variable spawning duration, and variable reproductive output are likely to strongly influence annual recruitment variability in E. chloroticus, with different larval subpopulations contributing unequally in different years. The ecological consequences of this, both for the ability of E. chloroticus to propagate itself in space and time and for the management of the developing E. chloroticus fishery in New Zealand, are discussed. Received: 9 December 1998 / Accepted: 13 June 2000     

Genetic structuring of <Emphasis Type="Italic">Latris lineata</Emphasis> at localized and transoceanic scales

Striped trumpeter (Latris lineata) is a demersal teleost distributed around the temperate clines of all the major oceans in the southern hemisphere. Within Tasmanian waters the species is managed as a single stock, although no studies have been performed to confirm genetic panmixia. A protracted pelagic larval phase and a recent transoceanic tag recapture of an adult fish suggest significant potential for genetic mixing between widely separated populations. Phylogenetic analysis of mitochondrial DNA control region sequences suggested no genetic mixing between Tasmania, New Zealand and St Paul/Amsterdam Islands, evidence for the first time that there is population structure at a transoceanic scale for this species. In addition, an analysis of molecular variance coupled with phylogenetic analyses suggested no significant structuring of striped trumpeter from three locations around Tasmania. The information provided in this study is useful for the design of modern fisheries management techniques such as spatially implemented marine reserves. In addition, species-by-species knowledge about population structures of marine species facilitates ecologically useful generalizations concerning their population dynamics and key issues on the broader ecology of the oceans.     

Marine biogeographic disjunction in central New Zealand

We present a phylogeographic analysis of an abundant New Zealand endemic sea-star, Patiriella regularis, to help pinpoint the location of an important biogeographic disjunction in central New Zealand. The analysis incorporates 284 mtDNA control region sequences (approximately 800 bp) of P. regularis from 22 coastal locations around New Zealand. We detected 132 haplotypes, with a mean divergence of 0.96%. AMOVA analysis of New Zealand samples is consistent with a north-south biogeographic disjunction across central New Zealand (among-group genetic variance=6.10%; P=0.0005). Cook Strait, the shallow marine strait separating the main islands, is not correlated with the disjunction: samples from northern South Island are genetically indistinguishable from North Island samples (variance=1.69%; P=0.073). These results are consistent with the hypothesis that upwelling zones south of Cook Strait constitute a significant barrier to larval dispersal.Communicated by M.S. Johnson, Crawley     

Microsatellite DNA markers and morphometrics reveal a complex population structure in a merobenthic octopus species (<Emphasis Type="Italic">Octopus maorum</Emphasis>) in south-east Australia and New Zealand

Five polymorphic microsatellite loci were developed and then used to assess the population genetic structure of a commercially harvested merobenthic octopus species (Octopus maorum) in south-east Australian and New Zealand (NZ) waters. Beak and stylet morphometrics were also used to assess population differentiation in conjunction with the genetic data. Genetic variation across all loci and all sampled populations was very high (mean number alleles = 15, mean expected heterozygosity = 0.85). Microsatellites revealed significant genetic structuring (overall F _ST = 0.024, p < 0.001), which did not fit an isolation-by-distance model of population differentiation. Divergence was observed between Australian and NZ populations, between South Australia and north-east Tasmania, and between two relatively proximate Tasmanian sites. South Australian and southern Tasmanian populations were genetically homogeneous, indicating a level of connectivity on a scale of 1,500 km. Morphometric data also indicated significant differences between Australian and NZ populations. The patterns of population structuring identified can be explained largely in relation to regional oceanographic features.     

Genetic heterogeneity among New Zealand species of hydrothermal vent mussels (Mytilidae: Bathymodiolus)

Molecular systematic studies provide evidence for three new species of Bathymodiolus-like hydrothermal vent mussels (Bivalvia: Mytilidae) from relatively shallow waters (depth less than 750 m) associated with the Kermadec Arc off northern New Zealand. Mitochondrial COI sequences from the three putative new species differed substantially from those of other known bathymodiolin species from the Pacific and Indian Oceans. Population genetic analysis of one of these species (Bathymodiolus new species NZ-1) revealed heterogeneity in allozyme gene frequencies between samples collected from two seamounts about 50 km apart. Factors that might contribute to genetic differentiation between neighbouring seamounts are discussed.Communicated by M.S. Johnson, Crawley     

Mitochondrial DNA and electronic tracking reveal population structure of Atlantic bluefin tuna (Thunnus thynnus)

Population subdivision was examined in Atlantic bluefin tuna (Thunnus thynnus) through sequencing of the control region of the mitochondrial genome. A total of 178 samples from the spawning grounds in the Gulf of Mexico, Bahamas and Mediterranean Sea were analyzed. Among the samples from these locations were 36 electronically tagged bluefin tuna that were tagged in the North Atlantic and subsequently traveled to one of these known spawning grounds during the spawning season. Bluefin tuna populations from the Gulf of Mexico and the Mediterranean Sea were found to be genetically distinct based on Φ_st, and sequence nearest neighbor analyses, showing that these two major spawning areas support independent stocks. Sequence nearest neighbor analysis indicated significant population subdivision among the Gulf of Mexico, western Mediterranean and eastern Mediterranean Sea. However, it was not possible to find significant pairwise differences between any sampling areas when using all samples. If only samples that had a high likelihood of assignment to a specific spawning site were used (young of the year, spawning adults), the differentiation increased among all sampling areas and the Western Mediterranean Sea was distinct from the Eastern Mediterranean Sea and the Gulf of Mexico. It was not possible to distinguish samples from the Bahamas from those collected at any of the other sampling sites. These data support tagging results that suggested distinctness of the Gulf of Mexico, Eastern and Western Mediterranean Sea spawning areas. This level of stock differentiation is only possible if Atlantic bluefin tuna show strong natal homing to individual spawning grounds.     

Low to moderate levels of genetic differentiation detected across the distribution of the New Zealand abalone, Haliotis iris

Two regions of the mitochondrial genome (cytochrome oxidase I and ATPase 8–ATPase 6) were used to examine the population genetic structure of New Zealand’s endemic abalone (Haliotis iris). Samples were collected from 28 locations around New Zealand between January 2005 and February 2008. At least four phylogeographic breaks were present and occurred across the Chatham rise, in the western Cook Strait region, along the southeast coast of the South Island, and at East Cape in the North Island. Gene flow across the Chatham rise is probably limited due to infrequent dispersal across large geographic distances (~850 km), while factors limiting gene flow around the North and South Islands are less clear, and understanding these may require intense temporal and spatial sampling in complex hydrographic regions. High genetic diversity and weak genetic structure may be a general feature of abalone potentially reflecting large and/or ancient populations.     

Genetic differentiation between morphotypes of the marine sponge Suberites ficus (Demospongiae: Hadromerida)

Sponges of three morphotypes of Suberites ficus (Johnston, 1842) were collected during February and March 1985 off the south-west of the Isle of Man, and were compared by using spicule size distributions and genetic allele frequencies of isozyme loci. The populations did not show any significant differences of spicule size or type, but could be easily differentiated into three separate species based on isozyme patterns. Samples of pale orange S. ficus growing on gastropod shells inhabited by hermit crabs (Pagurus spp.) were reproductively isolated from the redorange and the pale yellow colour morphs encrusting the bivalve Chlamys opercularis. These latter two colour morphs were genetically similar, but significant differences were observed at two of the 19 gene loci assayed. All the sponges studied were sympatric, and therefore the genetic differences, indicating reproductive isolation, are strong evidence for separate gene pools and, hence, that they are different species. The genetic identity between the two colour morphs of S. ficus on C. opercularis shells was 0.977, whilst between each of these and S. ficus on hermit crabs it was about 0.65. In all three species genetic variability was high, with mean expected and observed heterozygosity values per locus ranging from 0.17 to 0.36.