Stephen J. Newman

Phylogeography of the reef fish Cephalopholis argus(Epinephelidae) indicates Pleistocene isolation across the indo-pacific barrier with contemporary overlap in the coral triangle

BackgroundThe Coral Triangle (CT), bounded by the Philippines, the Malay Peninsula, and New Guinea, is the epicenter of marine biodiversity. Hypotheses that explain the source of this rich biodiversity include 1) the center of origin, 2) the center of accumulation, and 3) the region of overlap. Here we contribute to the debate with a phylogeographic survey of a widely distributed reef fish, the Peacock Grouper (Cephalopholis argus; Epinephelidae) at 21 locations (N = 550) using DNA sequence data from mtDNA cytochrome b and two nuclear introns (gonadotropin-releasing hormone and S7 ribosomal protein).ResultsPopulation structure was significant (ΦST = 0.297, P < 0.001; FST = 0.078, P < 0.001; FST = 0.099, P < 0.001 for the three loci, respectively) among five regions: French Polynesia, the central-west Pacific (Line Islands to northeastern Australia), Indo-Pacific boundary (Bali and Rowley Shoals), eastern Indian Ocean (Cocos/Keeling and Christmas Island), and western Indian Ocean (Diego Garcia, Oman, and Seychelles). A strong signal of isolation by distance was detected in both mtDNA (r = 0.749, P = 0.001) and the combined nuclear loci (r = 0.715, P < 0.001). We detected evidence of population expansion with migration toward the CT. Two clusters of haplotypes were detected in the mtDNA data (d = 0.008), corresponding to the Pacific and Indian Oceans, with a low level of introgression observed outside a mixing zone at the Pacific-Indian boundary.ConclusionsWe conclude that the Indo-Pacific Barrier, operating during low sea level associated with glaciation, defines the primary phylogeographic pattern in this species. These data support a scenario of isolation on the scale of 105 year glacial cycles, followed by population expansion toward the CT, and overlap of divergent lineages at the Pacific-Indian boundary. This pattern of isolation, divergence, and subsequent overlap likely contributes to species richness at the adjacent CT and is consistent with the region of overlap hypothesis.

Age, growth, mortality rates and corresponding yield estimates using otoliths of the tropical red snappers, Lutjanus erythropterus, L. malabaricus and L. sebae, from the central Great Barrier Reef☆

Abstract Otoliths of L. erythropterus, L. malabaricus and L. sebae from the central Great Barrier Reef contain a well defined series of opaque and translucent increments known to be deposited annually. These three species are relatively long-lived, and grow slowly after becoming reproductively mature. Age estimates up to 32 years for L. erythropterus, 20 years for L. malabaricus and 22 years for L. sebae were much higher than those previously reported from other northern Australian waters. Age estimates obtained from counts of increments on whole otoliths were consistently much lower and more imprecise, at all ages compared with counts from sectioned otoliths. Precision of counts from whole otoliths declined significantly with increasing fish age. The regression of sectioned age on otolith weight revealed consistent linear relationships among all three species. To explore the fishery research and management implications of these biases, age estimates from the two ageing methods were used to construct comparative growth and mortality parameters and model yield-per-recruit values under contrasting harvest strategies. While the von Bertalanffy growth functions were not significantly different for the two methods, the underestimates of age from whole otoliths caused serious over-estimation of natural mortality. Serious overfishing could occur if these estimates were applied for fishery management purposes.

Age validation, growth and mortality rates of the tropical snappers (Pisces: Lutjanidae) Lutjanus adetii (Castelnau, 1873) and L. quinquelineatus (Bloch, 1790) from the central Great Barrier Reef, Australia

The age and growth of Lutjanus adetii and L. quinquelineatus from the central Great Barrier Reef were determined from studies of annuli in sectioned otoliths (sagittae). The period of annulus formation was validated by oxytetracycline labelling of externally tagged fishes. For L. adetii, validation was obtained from tagged fishes that were recaptured after a minimum of 12 months at liberty, the first time this has been achieved for a Lutjanus species. A single opaque and translucent zone was formed once a year, with the opaque band (annulus) being formed during the winter months. Otolith weight was strongly correlated with age for both species. There was significant differential growth between the sexes in length-at-age and weight-at-age for both species, with males growing larger than females. The oldest individuals found were a male L. adetii of 24 years of age and a female L. quinquelineatus of 31 years of age. The shape of the growth curves were steep for the first few years and then became asymptotic. The annual instantaneous rate of natural mortality (M) was 0.235 for L. adetii and 0.154 for L. quinquelineatus, representing an annual survivorship of 79% and 86%, respectively. The protracted longevity and low natural mortality rates imply that both L. adetii and L. quinquelineatus are vulnerable to overfishing despite their small size.

Bait Effects in Sampling Coral Reef Fish Assemblages with Stereo-BRUVs

Baited underwater video techniques are increasingly being utilised for assessing and monitoring demersal fishes because they are: 1) non extractive, 2) can be used to sample across multiple habitats and depths, 3) are cost effective, 4) sample a broader range of species than many other techniques, 5) and with greater statistical power. However, an examination of the literature demonstrates that a range of different bait types are being used. The use of different types of bait can create an additional source of variability in sampling programs. Coral reef fish assemblages at the Houtman Abrolhos Islands, Western Australia, were sampled using baited remote underwater stereo-video systems. One-hour stereo-video recordings were collected for four different bait treatments (pilchards, cat food, falafel mix and no bait (control)) from sites inside and outside a targeted fishery closure (TFC). In total, 5209 individuals from 132 fish species belonging to 41 families were recorded. There were significant differences in the fish assemblage structure and composition between baited and non-baited treatments (P<0.001), while no difference was observed with species richness. Samples baited with cat food and pilchards contained similar ingredients and were found to record similar components of the fish assemblage. There were no significant differences in the fish assemblages in areas open or closed to fishing, regardless of the bait used. Investigation of five targeted species indicated that the response to different types of bait was species-specific. For example, the relative abundance of Pagrus auratus was found to increase in areas protected from fishing, but only in samples baited with pilchards and cat food. The results indicate that the use of bait in conjunction with stereo-BRUVs is advantageous. On balance, the use of pilchards as a standardised bait for stereo-BRUVs deployments is justified for use along the mid-west coast of Western Australia.

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.

Bomb radiocarbon dating of three important reef-fish species using Indo-Pacific D14C chronologies

Demersal reef fishes of the Indo-Pacific are under increasing pressure as a fisheries resource, yet many of the important life history characteristics required for suitable management are poorly known. The three fish species, eightbar grouper (Hyporthodus octofasciatus), ruby snapper (Etelis carbunculus) and the spangled emperor (Lethrinus nebulosus), are important components of fisheries and ecosystems throughout the Indo-Pacific. Despite their importance, age and growth information is incomplete. Age has been estimated for E. carbunculus and L. nebulosus, but validated age beyond the first few years is lacking and for H. octofasciatus no age estimates exist. Bomb radiocarbon dating can provide age estimates that are independent of growth-zone counting, but only if appropriate reference Δ14C chronologies exist. In this study, a series of Δ14C records from hermatypic corals was assembled to provide a basis for bomb radiocarbon dating in the western Indo-Pacific region. Results provided (1) valid age estimates for comparison to age estimates from two facilities investigating growth-zones in otolith thin sections; (2) support for age estimation protocols using otolith thin sections; and (3) the information necessary for further refinement of age estimation procedures. Estimates of longevity from bomb radiocarbon dating agree with some prior studies: H. octofasciatus, E. carbunculus and L. nebulosus all being long-lived species with life spans of at least 43, 35 and 28 years respectively.

Limited ecological population connectivity suggests low demands on self-recruitment in a tropical inshore marine fish (Eleutheronema tetradactylum: Polynemidae)

The diversity of geographic scales at which marine organisms display genetic variation mirrors the biophysical and ecological complexity of dispersal by pelagic larvae. Yet little is known about the effect of larval ecology on genetic population patterns, partly because detailed data of larval ecology do not yet exist for most taxa. One species for which this data is available is Eleutheronema tetradactylum, a tropical Indo‐West Pacific shorefish. Here, we use a partial sequence mitochondrial cytochrome oxidase subunit 1 (COI) marker and five microsatellite loci to survey the genetic structure of E. tetradactylum across northern Australia. Structure was found throughout the range and isolation by distance was strong, explaining approximately 87 and 64% of the genetic variation in microsatellites and mtDNA, respectively. Populations separated by as little as 15 km also showed significant genetic structure, implying that local populations are mainly insular and self‐seeding on an ecological time frame. Because the larvae of E. tetradactylum have lower swimming performance and poor orientation compared with other tropical fishes, even modest larval abilities may permit self‐recruitment rather than passive dispersal.

Understanding age-specific dispersal in fishes through hydrodynamic modelling, genetic simulations and microsatellite DNA analysis.

Many marine species have vastly different capacities for dispersal during larval, juvenile and adult life stages, and this has the potential to complicate the identification of population boundaries and the implementation of effective management strategies such as marine protected areas. Genetic studies of population structure and dispersal rarely disentangle these differences and usually provide only lifetime‐averaged information that can be considered by managers. We address this limitation by combining age‐specific autocorrelation analysis of microsatellite genotypes, hydrodynamic modelling and genetic simulations to reveal changes in the extent of dispersal during the lifetime of a marine fish. We focus on an exploited coral reef species, Lethrinus nebulosus, which has a circum‐tropical distribution and is a key component of a multispecies fishery in northwestern Australia. Conventional population genetic analyses revealed extensive gene flow in this species over vast distances (up to 1500 km). Yet, when realistic adult dispersal behaviours were modelled, they could not account for these observations, implying adult dispersal does not dominate gene flow. Instead, hydrodynamic modelling showed that larval L. nebulosus are likely to be transported hundreds of kilometres, easily accounting for the observed gene flow. Despite the vast scale of larval transport, juvenile L. nebulosus exhibited fine‐scale genetic autocorrelation, which declined with age. This implies both larval cohesion and extremely limited juvenile dispersal prior to maturity. The multidisciplinary approach adopted in this study provides a uniquely comprehensive insight into spatial processes in this marine fish.

Maturation and sexual ontogeny in the spangled emperor Lethrinus nebulosus

The reproductive development and sexual ontogeny of spangled emperor Lethrinus nebulosus populations in the Ningaloo Marine Park (NMP) were investigated to obtain an improved understanding of its evolved reproductive strategy and data for fisheries management. Evidence derived from (1) analyses of histological data and sampled sex ratios with size and age, (2) the identification of residual previtellogenic oocytes in immature and mature testes sampled during the spawning season and (3) observed changes in testis internal structure with increasing fish size and age, demonstrated a non-functional protogynous hermaphroditic strategy (or functional gonochorism). All the smallest and youngest fish sampled were female until they either changed sex to male at a mean 277.5 mm total length (L(T)) and 2.3 years old or remained female and matured at a larger mean L(T) (392.1 mm) and older age (3.5 years). Gonad masses were similar for males and females over the size range sampled and throughout long reproductive lives (up to a maximum estimated age of c. 31 years), which was another correlate of functional gonochorism. That the mean L(T) at sex change and female maturity were below the current minimum legal size (MLS) limit (410 mm) demonstrated that the current MLS limit is effective for preventing recreational fishers in the NMP retaining at least half of the juvenile males and females in their landed catches.

Calibration of pelagic stereo‐BRUVs and scientific longline surveys for sampling sharks

Summary Our understanding of the ecology of sharks and other highly mobile marine species often relies on fishery-dependent data or extractive fishery-independent techniques that can result in catchability and size-selectivity biases. Pelagic Baited Remote Underwater stereo-Video Systems (pelagic stereo-BRUVs) provide a standardized, non-destructive and fishery-independent approach to estimate biodiversity measures of fish assemblages in the water column. However, the performance of this novel method has not yet been assessed relative to other standard sampling techniques. We compared the catch composition, relative abundance and length distribution of fish assemblages sampled using pelagic stereo-BRUVs and conventional scientific longline surveys. In particular, we focused on sharks of the family Carcharhinidae (requiem sharks) to assess the sampling effectiveness of this novel technique along a latitudinal gradient off the coast of Western Australia. We calibrated the sampling effort required for each technique to obtain equivalent samples of the target species and discuss the advantages, limitations and potential use of these methods to study highly mobile species. The proportion of sharks sampled by pelagic stereo-BRUVs and scientific longline surveys was comparable across the latitudinal gradient. Carcharhinus plumbeus was the most abundant species sampled by both the techniques. Longline surveys selected larger individuals of the family Carcharhinidae in comparison with the length distribution data obtained from pelagic stereo-BRUVs. However, the relative abundance estimates (catch per unit of effort) from the pelagic stereo-BRUVs were comparable to those from 5 to 30 longline hooks. Pelagic stereo-BRUVs can be calibrated to standard techniques in order to study the species composition, behaviour, relative abundance and size distribution of highly mobile fish assemblages at broad spatial and temporal scales. This technique offers a non-destructive fishery-independent approach that can be implemented in areas that may be closed to fishing and is suitable for studies on rare or threatened species.