Cover Caption

Cover: Examples of color variation in five broadly distributed coral reef fishes. Historically these variants were considered the same species; however, genetic analyses reveal the populations from Fiji are a unique evolutionary lineage. Their uniqueness suggests that diversity of fishes in the Pacific has been underestimated and that biodiversity may be highly regionalized (photos by Gerry Allen). See pages 965–975.     

Genetic connectivity among color morphs and Pacific archipelagos for the flame angelfish, <Emphasis Type="Italic">Centropyge loriculus</Emphasis>

Color variation is used in taxonomic classification of reef fishes, but it may not reliably indicate evolutionary divergence. In the central Pacific, there are three color morphs of the flame angelfish, Centropyge loriculus: a red morph that occurs primarily in the Hawaiian archipelago, the endemic Marquesan color morph with reduced black markings, and an orange morph that occurs throughout the rest of Oceania. The red and orange morphs co-occur at Johnston Atoll (1,300 km south of Hawai’i), but intermediate forms have not been reported. To determine whether the three color morphs represent distinct evolutionary lineages, we compared 641 base pairs of mitochondrial cytochrome b. Forty-one closely related haplotypes were observed in 116 individuals. Analysis of molecular variance (AMOVA) indicated no significant genetic structure among color morphs (Φ_ST = 0.011, P = 0.147). Likewise, there was no significant pairwise structure between sampling locations, separated by up to 5,700 km, after a Bonferroni correction (Φ_ST = 0.000–0.080, P = 0.0130–0.999). Genetic studies in conjunction with larval distribution data indicate that Centropyge species are highly dispersive. While there is a strong geographic component to the distribution of color morphs in C. loriculus, we find no evidence for corresponding genetic partitioning. We do not rule out an adaptive role for color differentiation, but our data do not support emerging species.     

Connectivity between marine reserves and exploited areas in the philopatric reef fish Chrysoblephus laticeps (Teleostei: Sparidae)

‘No-take’ marine protected areas (MPAs) are successful in protecting populations of many exploited fish species, but it is often unclear whether networks of MPAs are adequately spaced to ensure connectivity among reserves, and whether there is spillover into adjacent exploited areas. Such issues are particularly important in species with low dispersal potential, many of which exist as genetically distinct regional stocks. The roman, Chrysoblephus laticeps, is an overexploited, commercially important sparid endemic to South Africa. Post-recruits display resident behavior and occupy small home ranges, making C. laticeps a suitable model species to study genetic structure in marine teleosts with potentially low dispersal ability. We used multilocus data from two types of highly variable genetic markers (mitochondrial DNA control region and seven microsatellite markers) to clarify patterns of genetic connectivity and population structure in C. laticeps using samples from two MPAs and several moderately or severely exploited regions. Despite using analytical tools that are sensitive to detect even subtle genetic structure, we found that this species exists as a single, well-mixed stock throughout its core distribution. The high levels of connectivity identified among sites support the findings of previous studies that have indicated that inshore MPAs are an adequate tool for managing overexploited temperate reef fishes. Even though dispersal of adult C. laticeps out of MPAs is limited, the fact that the large adults in these reserves produce exponentially more offspring than their smaller counterparts in exploited areas makes MPAs a rich source of recruits. We nonetheless caution against concluding that the lack of structure identified in C. laticeps and several other southern African teleosts can be considered to be representative of marine teleosts in this region in general. Many such species are represented in more than one marine biogeographic province and may be comprised of regionally adapted stocks that require individual management.     

Understanding origins of present-day genetic structure in marine fish: biologically or historically driven patterns?

Determining the origin of genetic structure is of wide interest because of its use in stock discrimination in marine organisms. Schematically, genetic differentiation can result from historical patterns maintained over geological time or from present-day isolation attributable to biological characteristics of the species. We used a comparative approach to population genetic analysis based on allozyme polymorphism to determine the impact of reproductive strategy (i.e. biological origin) and habitat (i.e. historical origin) on the genetic structure of individuals sampled from five isolated islands in French Polynesia. Eight species of coral reef fishes from two families (Chaetodontidae and Pomacentridae) were selected to test the impact of sea-level change (historical origin) and reproductive strategy (biological origin) on genetic structure. Seven of the eight study species showed significant divergence in allelic frequencies computed over all sites. For these seven species, multilocus F_stvalues ranged from 0.0114 to 0.0287. None of the eight species showed a significant relationship between genetic divergence and geographical distance between sites. Significant divergence (difference in allozyme frequencies) between some pairs of sites occurred but was unrelated to distances between them. These results suggest that the genetic structure of coral reef fish in French Polynesia is likely to be driven according to an island model in which migrations between populations are rare and random in space and time. Overall, none of the species showed congruent genetic structures between sites sampled. Genetic structure of the eight species did not appear significantly related either to reproductive strategy or habitat preference. Genetic diversity (heterozygosity) was significantly correlated with these two factors, with species laying benthic eggs and/or inhabiting lagoons showing significantly higher multilocus heterozygosity than species laying pelagic eggs and/or living on the outer reef slope. Overall, the absence of differences according to habitat and/or reproductive strategy did not provide any conclusive pattern regarding the origin of the genetic structure, but the limited divergence in allelic frequencies suggests recent differentiations.     

Minimal genetic variation among samples of six species of coral reef fishes collected at La Parguera,Puerto Rico,and Discovery Bay,Jamaica

Intraspecific genetic variation among samples of six species of reef fishes,Chromis cyanea, Stegastes partitus, S. planifrons, S. leucostictus, S. dorsopunicans, andThalassoma bifasciatum collected over a 2 wk period in 1990 at La Parguera, Puerto Rico, USA and Discovery Bay, Jamaica, was evaluated using starch-gel electrophoresis. On average, products of 33 protein-coding loci were resolved in each species. Levels of polymorphism (0.95 criterion) ranged from 3.1% inS. dorsopunicans to 42.4% inC. cyanea. Estimates of genetic divergence among samples and indices of genetic subdivision were small in all six study species: mean genetic distances ranged from 0.000 to 0.002 and mean fixation indices ranged from 0.004 to 0.035. Estimates of numbers of migrants per generation (mN _e) ranged from 5.1 to 11.6, indicating that substantial genetic exchange probably occurs over the relatively large geographic distance (ca. 1000 km) separating coral reef communities of La Parguera and Discovery Bay. The estimates ofmN _e may be biased by a sampling strategy involving only two localities, and should therefore be interpreted with caution. With inferences based solely on allozyme frequency data under a primary assumption of neutrality, genetic substructuring of populations of the six study species on a macrogeographic scale appears virtually nonexistent.     

Association of color and feeding deterrence by tropical reef fishes

Summary. While many marine molluscs have been suggested to use aposematic coloration to avoid predation, few studies have tested the ability of marine predators to learn to associate colors with distasteful prey. In field experiments, we tested the ability of two populations of reef fishes to discriminate among red, yellow, and black artificial nudibranch models when one color was paired with a feeding deterrent. We offered fishes (1) the models without any feeding deterrents, (2) the models with a feeding deterrent coated onto one color, and (3) the models without deterrents again. If reef fishes learn to associate colors with noxious prey, we expected the color paired with the feeding deterrent to be eaten less frequently in the final assay than the initial assay. In both populations, fishes formed clear associations between color and feeding deterrence. However, when the experiment was repeated in one population, changing the color paired with the feeding deterrent, fishes did not form an association between color and feeding deterrence. In this case, prior learning may have affected subsequent trials. Our study indicates that common colors of nudibranchs are recognizable by fishes and can be associated with noxious prey. Received 24 September 1998; accepted 18 December 1998.     

Tolerance to high temperatures and potential impact of sea warming on reef fishes of Gorgona Island (tropical eastern Pacific)

Knowledge of upper thermal-tolerance limits of marine organisms in the tropical eastern Pacific (TEP) is important because of the influence of phenomena such as El Niño and global warming, which increase sea temperature. Laboratory experiments were conducted to determine the critical thermal maximum (CTM) of reef fishes from the TEP. In 15 reef fishes of Gorgona Island (TEP) the CTM was between 34.7°C and 40.8°C. None of these CTMs was exceeded by sea temperature in the TEP during any of the strongest El Niño events in this century (32°C during El Niño 1982-1983 and 1997-1998), which indicates that all species studied here may tolerate El Niño maximum temperatures. In addition, the CTM of the least-tolerant species was 8°C above the current mean sea temperature in a wide range of latitudes in the TEP. This suggests that fishes live far from their upper thermal tolerance limits and that the current global-warming trend is still unlikely to be dangerous for these species. If sea temperature continues to increase at the current rate, in about a century sea temperature could exceed the thermal tolerance of some reef fishes and threaten them with extinction. Such risk, however, might occur sooner if the sea temperature during El Niño also increased in step with the global warming, but also because other processes involved in maintaining population, such as reproduction, can be affected at lower temperatures. The possible ability of reef fishes to adapt to increases in sea temperature is discussed.     

Variation in larval life-history traits among reef fishes across the Isthmus of Panama

We tested the hypothesis that regional differences in oceanic productivity have led to the evolution of predictable patterns of regional variation in life-history traits of pelagic larvae of tropical reef fishes. To do so we compared larval traits (egg and hatchling size, larval growth rate and duration, and size at settlement) among closely related reef fishes from the Atlantic and Pacific coasts of the Isthmus of Panama. This comparison provides a control for phylogenetic effects because those regions shared a common fauna prior to the rise of the Isthmus ˜3.5 million years ago, subsequent to which each fauna evolved independently under a very different productivity regime. We measured larval traits of 12 benthic-spawning damselfishes (Pomacentridae: Abudefduf, Chromis and Stegastes) and 13 pelagic-spawning wrasses (Labridae: Bodianus, Halichoeres and Thalassoma). These included members of each genus on each side of the Isthmus and four sets of transisthmian sister species of pomacentrids. Among the pomacentrids we found consistent transisthmian differences in hatchling size, but not in other larval traits. Essentially the reverse pattern occurred among the labrids – larval growth and duration differed consistently among congeners in the two regions, but without consistent differences in hatchling size or size at settlement. Neither relationship is predicted by the regional-productivity hypothesis. Most of the differences were quite small. Stronger phylogenetic effects on larval traits (inter- and intrageneric variation within regions) occur in both families and evidently overwhelm any effect of regional variation in productivity. Reassessment of data that takes into account such phylogenetic effects questions previous conclusions about the existence of regional differences in larval traits among damselfishes in the West Pacific and the Caribbean. Received: 19 January 2000 / Accepted: 26 September 2000     

New insight on population genetic connectivity of widespread amphidromous prawn Macrobrachium lar (Fabricius, 1798) (Crustacea: Decapoda: Palaemonidae)

Due to the sparse and unstable nature of insular freshwater habitats, marine larval dispersal of amphidromous species is considered a critical element of population persistence. We assessed population genetic structure of freshwater prawn Macrobrachium lar across its range that encompasses two biogeographic barriers: the vast open ocean separating Western and Central Pacific regions and the Indo-Malay archipelago separating Indian and Pacific oceans. A total of 173 samples collected from 21 islands throughout the Indo-Pacific were sequenced at 16S and 28S rDNA. We observed distinct genetic isolation of populations located at the eastern and southwestern edge of the species range but no evidence of an effect of the Indo-Pacific barrier. Differentiation patterns are consistent with a stepping-stone model of dispersal. Genetic differences of Central Pacific populations may reflect founder events associated with colonization of isolated islands, or be a signature of a past bottleneck after population depletion caused by drastic climatic events.     

Isolation and population divergence of a widespread Indo-West Pacific marine gastropod at Easter Island

Oceanic islands represent excellent systems for studying the link between geographic isolation and population divergence. Easter Island is the world’s most isolated island and exhibits a high level of endemicity in the nearshore marine environment. Yet few studies have examined the effect of such extreme isolation on the divergence of populations of widespread species that occur at Easter Island. Conus miliaris, a marine gastropod distributed throughout much of the Indo-West Pacific, occurs at Easter Island where the population is ecologically and morphologically distinct from other populations of the species. To determine whether these phenotypic differences are associated with genetic isolation of the Easter Island population, we investigated the phylogeography of this species by examining mitochondrial COI sequences obtained from 141 individuals from eight localities occurring predominantly in the western, central and southeastern Pacific. Results from our analyses show that C. miliaris at Easter Island differs genetically from other populations. We estimate that C. miliaris colonized Easter Island shortly after the origin of the island ≤0.7 million years ago and that since population founding, gene flow has occurred predominantly from Easter Island to the west and that little migration has occurred into Easter Island.     

Extreme genetic diversity and temporal rather than spatial partitioning in a widely distributed coral reef fish

Mitochondrial control region (HVR-1) sequences were used to identify patterns of genetic structure and diversity in Naso vlamingii, a widespread coral reef fish with a long evolutionary history. We examined 113 individuals from eight locations across the Indo-Pacific Ocean. Our aims were to determine the spatial scale at which population partitioning occurred and then to evaluate the extent to which either vicariance and/or dispersal events have shaped the population structure of N. vlamingii. The analysis produced several unexpected findings. Firstly, the genetic structure of this species was temporal rather than spatial. Secondly, there was no evidence of a barrier to dispersal throughout the vast distribution range. Apparently larvae of this species traverse vicariance barriers that inhibit inter-oceanic migration of other widespread reef fish taxa. Thirdly, an unusual life history and long evolutionary history was associated with a population structure that was unique amongst coral reef fishes in terms of the magnitude and pattern of genetic diversity (haplotype diversity, h = 1.0 and nucleotide diversity π = 13.6%). In addition to these unique characteristics, there was no evidence of isolation by distance (r = 0.458, R ² = 0.210, P = 0.078) as has also been shown for some other widespread reef species. However, some reductions in gene flow were observed among and within Ocean basins [Indian–Pacific analysis of molecular variance (AMOVA), Φ _st = 0.0766, P < 0.05; West Indian–East Indian–Pacific AMOVA Φ _st = 0.079, P < 0.05]. These findings are contrasted with recent studies of coral reef fishes that imply a greater degree of spatial structuring in coral reef fish populations than would be expected from the dispersive nature of their life cycles. We conclude that increased taxon sampling of coral reef fishes for phylogeographic analysis will provide an extended view of the ecological and evolutionary processes shaping coral reef fish diversity at both ends of the life history spectrum.     

High genetic diversities and complex genetic structure in an Indo-Pacific tropical reef fish (Chlorurus sordidus): evidence of an unstable evolutionary past?

Historical sea level fluctuations have influenced the genetic structure and evolutionary history of marine species and examining widespread species across their species ranges may elucidate some of these effects. Chlorurus sordidus is a common and widespread parrotfish found on coral reefs throughout the Indo-central Pacific. We used phylogenetic, phylogeographic, and cladistic analyses to examine the genetic composition and population structure of this species across most of its latitudinal range limits. We sequenced 354 bp of the mitochondrial control region I in 185 individuals from nine populations. Populations of C. sordidus displayed high levels of genetic diversity, similar to those recorded for widespread pelagic fish species, but much greater nucleotide diversity values than those previously recorded for other demersal reef fishes. Both phylogenetic and phylogeographic analyses detected strong genetic subdivision at the largest spatial scale (i.e. among oceans). The Pacific Ocean was characterised by weak population genetic structure. Separation of the Hawaiian location from other Pacific and West Indian Ocean sites was evident in phylogenetic analyses, but not from analysis of molecular variance. NCA and isolation-by-distance tests suggested that the genetic structure of this species was the result of multiple contemporary and historical processes, including long-distance colonisation and range expansion arising from fluctuating sea levels, limited current gene flow, and isolation by distance. This pattern is to be expected when historically fragmented populations come into secondary contact. We suggest the patterns of population genetic structure recorded in C. sordidus are caused by large local population sizes, high gene flow, and a recent history of repeated fragmentation and remixing of populations resulting from fluctuating sea levels.Communicated by M.S. Johnson, Crawley     

Regional differences in duration of the planktonic larval stage of reef fishes in the eastern Pacific Ocean

Regional variation in the duration of the planktonic larval phase of three species of reef fishes, Thalassoma lucasanum (Labridae), Stegastes flavilatus, and Microspathodon dorsalis (Pomacentridae) was investigated between 1982 and 1991 at several sites in the tropical eastern Pacific over a distance of 3500 km, encompassing virtually their entire range of distribution. Durations of the larval phase, determined from counts of daily otolith increments, were significantly different (1.3 to 1.6 x) between sites. Populations of all three species had a consistently shorter larval life at the most northern site, Cabo San Lucas (Mexico) compared to Panamá and the offshore islands of Galápagos and Cocos. Analyses of otolith increment width over the precompetent period revealed that this disparity in larval duration primarily reflected differences in larval growth rates: faster growing fish spent less time in the plankton. In T. lucasanum, some of the variation in larval duration between Panamá and offshore sites (Galápagos Islands and Cocos Island) may be accounted for by a higher frequency of individuals delaying metamorphosis at the offshore sites. These data indicate that conditions in the planktonic environment are not homogeneous throughout the tropical eastern Pacific and may have a profound effect on aspects of the larval ecology of reef fishes in this region.     

Phylogeography of the seaweed Ishige okamurae (Phaeophyceae): evidence for glacial refugia in the northwest Pacific region

Although benthic marine algae are essential components of marine coastal systems that have been influenced profoundly by past and present climate change, our knowledge of seaweed phylogeography is limited. The brown alga Ishige okamurae Yendo occurs in the northwest Pacific, where it occupies a characteristic belt in the exposed intertidal zone. To understand the patterns of genetic diversity and the evolutionary history of this species, we analyzed mitochondrial cox3 from 14 populations (221 individuals) throughout its range. The 17 haplotypes found in this study formed five distinct clades, indicating significant genetic structure. The high differentiation and number of unique (private) haplotypes may result from the recolonization of the species from glacial refugia. Three putative refugia, each with high genetic diversity, were identified: southern Korea (including Jeju Island), northern Taiwan, and central Pacific Japan. Recolonization of I. okamurae was probably determined by ocean currents and changes in sea level during the last glacial period.     

Species boundaries in the starfish genus Linckia

 The genetic basis for species boundaries in the starfish genus Linckia was examined using variation observed in 613 base pairs (bp) of sequence from the cytochrome oxidase I gene of mtDNA and 16 allozyme loci. Five groups within Linckia were clearly genetically differentiated; L. columbiae, L. bouvieri, two clades within L. guildingi, and one clade with two sub-clades consisting of both L. laevigata and L. multifora. Genetic divergence among these groups is consistent with interspecific variation. The two clades within L. guildingi suggest the presence of a cryptic, partially sympatric, species. Genetic divergence between these two clades implies that they have been genetically distinct from each other for at least one million years. In contrast, genetic data suggest that L. laevigata and L. multifora are a single species, despite the fact that live individuals can be distinguished by their colour and colour pattern, number of madreporites and ratio of arm length to breadth. There are probably three closely related groups within the L. laevigata/L. multifora clade –L. multifora, and two groups in L. laevigata defined by biogeographic province. It is difficult to determine boundaries for these three entities, since genetic and morphological differences are complicated by phenotypic differences arising from both environmental variation and population genetic structure. The difficulties encountered in defining species boundaries in Linckia, particularly with respect to variation arising from the overlap of Indian and Pacific biogeographic provinces, may be a general issue for many marine organisms from this region. Received: 24 May 1999 / Accepted: 6 October 1999     

Population genetics of eight species of Trapezia (Brachyura: Xanthidae), symbionts of corals

Starch-gel electrophoresis was used to study gene-enzyme variation in thirteen populations of eight species of the genus Trapezia from Hawaii, Panamá, and Enewetak Atoll (Marshall Islands). Between 20 and 30 (mean = 27.8) gene-enzyme systems were resolved in each population, with 20 systems in common among all populations. The distribution of electrophenotypes was in agreement with Hardy-Weinberg-Castle expectations, except for T. digitalis, which consistently showed heterozygote deficiencies. Diagnostic loci among color forms support the hypothesis that color forms are distinct species. Low values of genetic distance among species suggest a recent radiation, perhaps during the Pleistocene. Genetic distance between the Hawaiian and Panamanian populations of T. ferruginea did not significantly differ from zero, indicating that the Eastern Pacific population of T. ferruginea has recently immigrated from the central Pacific, and/or that there is gene flow between the two areas. There were diagnostic loci between T. ferruginea and T. formosa from Enewetak and the populations of these species from Hawaii (T. ferruginea only) and Panamá (both species). Therefore, these geographic populations may represent separate species. The level and pattern of genetic variability in Trapezia spp. are in agreement with those observed in most other organisms.     

Gene flow at three spatial scales in a coral reef fish, the three-spot dascyllus, Dascyllus trimaculatus

Dispersal in coral reef fishes occurs predominantly during the larval planktonic stage of their life cycle. With relatively brief larval stages, damselfishes (Pomacentridae) are likely to exhibit limited dispersal. This study evaluates gene flow at three spatial scales in one species of coral reef damselfish, Dascyllus trimaculatus. Samples were collected at seven locations at Moorea, Society Islands, French Polynesia. Phylogenetic relationships and gene flow based on mitochondrial control region DNA sequences between these locations were evaluated (first spatial scale). Although spatial structure was not found, molecular markers showed clear temporal structure, which may be because pulses of settling larvae have distinct genetic composition. Moorea samples were then compared with individuals from a distant island (750 km), Rangiroa, Tuamotu Archipelago, French Polynesia (second spatial scale). Post-recruitment events (selection) and gene flow were probably responsible for the lack of structure observed between populations from Moorea and Rangiroa. Finally, samples from six Indo-West Pacific locations, Zanzibar, Indonesia, Japan, Christmas Island, Hawaii, and French Polynesia were compared (third spatial scale). Strong population structure was observed between Indo-West Pacific populations. Received: 26 May 2000 / Accepted: 10 October 2000     

High levels of genetic subdivision of marine and estuarine populations of the estuarine catfishCnidoglanis macrocephalus (Plotosidae) in southwestern Australia

The cobblerCnidoglanis macrocephalus (Valenciennes) is an endemic marine and estuarine catfish from southern Australia. Conflicting views on the degree of isolation of the estuarine populations underscore general questions about genetic divergence in coastal species. Although estuaries are widely recognized as ecologically important, little work has been done on their role in favouring genetic divergence. In order to estimate the extent of genetic subdivision among nearshore marine and estuarine populations, electrophoretic variation of enzymes was examined in seven marine and six estuarine populations of cobbler from sites spanning 1500 km along the southwest Australian coastline. Among all populations, the mean standardized variance in allelic frequencies (F _ST) for six polymorphic loci was 0.277, a high value comparable to those of other shallow-water teleosts whose life-history characteristics and habitat preferences restrict their dispersal capability. The pattern of genetic identities between populations showed divergence between west and south coast sites. Within these regional groups, however, there was substantial heterogeneity, much of which was associated with estuaries. Among all six estuarine sites, the averageF _ST was 0.333, 40% higher than the value of 0.237 for the marine sites. Low estimates of the genetically effective number of migrants suggest population subdivision between marine and estuarine environments and between similar habitat types. This study indicates the importance of habitat in affecting the connectedness of populations, even in apparently open marine systems.     

Territorial User Rights for Fisheries as Ancillary Instruments for Marine Coastal Conservation in Chile

Territorial user rights for fisheries have been advocated as a way to achieve sustainable resource management. However, few researchers have empirically assessed their potential as ancillary marine conservation instruments by comparing them to no‐take marine protected areas. In kelp (Lessonia trabeculata) forests of central Chile, we compared species richness, density, and biomass of macroinvertebrates and reef fishes among territorial‐user‐right areas with low‐level and high‐level enforcement, no‐take marine protected areas, and open‐access areas in 42 100‐m subtidal transects. We also assessed structural complexity of the kelp forest and substratum composition. Multivariate randomized permutation tests indicated macroinvertebrate and reef fish communities associated with the different access regimes differed significantly. Substratum composition and structural complexity of kelp forest did not differ among access regimes. Univariate analyses showed species richness, biomass, and density of macroinvertebrates and reef fishes were greater in highly enforced territorial‐user‐right areas and no‐take marine protected areas than in open‐access areas. Densities of macroinvertebrates and reef fishes of economic importance were not significantly different between highly enforced territorial‐user‐right and no‐take marine protected areas. Densities of economically important macroinvertebrates in areas with low‐level enforcement were significantly lower than those in areas with high‐level enforcement and no‐take marine protected areas but were significantly higher than in areas with open access. Territorial‐user‐right areas could be important ancillary conservation instruments if they are well enforced. Derechos de Usuario Territoriales para Pesquerías como Instrumentos Accesorios para la Conservación Marina Costera en Chile     

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.