Genetic effective population size (Nₑ) estimators are useful as applied conservation tools. Many elasmobranch (shark and ray) species are threatened at local and global scales, and tools to monitor ...these populations are greatly needed. This study investigates contemporary Nₑ and its relationship with census size (Nc) in a population of zebra sharks (Stegostoma fasciatum). Our Nₑ using the linkage disequilibrium method, 377 (95 % CI 274–584) was found to closely approximate the mark-recapture Nc for this population of mature sharks (458, 95 % CI 298–618), with an Nₑ/Nc ratio of 0.82 (SE = 0.33). Furthermore, we conducted a series of sensitivity analyses to examine how the numbers of samples and loci affect the precision and accuracy of the estimators. We demonstrate that for this species robust and precise estimates are obtainable with a minimum of 91 samples (approximately 20 % of the census population) and 10 microsatellite loci. These findings contribute important information to the greater body of Nₑ and Nₑ/Nc relationships in elasmobranchs and wildlife populations as well as provide important guidelines for implementing genetic monitoring in elasmobranch conservation efforts.
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 size and structure of a photographically identified population of reef manta ray,
Manta alfredi
, were examined at aggregation sites over a four-year period in southern Mozambique. The use and ...standardisation of photo-ID techniques was examined as a minimally-intrusive means to study this species. Using these techniques, we report on the size, structure and seasonality of this population of
M. alfredi
. In total, 449 individuals were identified during this time period, 40.5% of which were re-sighted on at least one occasion. The longest period between re-sighting events was 1,252 days. During the study period, annual population size estimates for
M.
alfredi
ranged from 149 to 454 individuals. The superpopulation size estimate for the entire study period was 802 individuals, the first reported for
M. alfredi
at a monitored aggregation site. A highly significant sex bias was evident with a female:male ratio of 3.55:1. The majority of rays (89.9% males; 49.7% females) were considered mature, with most individuals between 3.0 and 4.9 m in disc width.
Manta alfredi
were observed at the study sites in each month of the calendar year. The maximum number of individual rays seen per dive was 30. Large numbers of rays (20 + per dive) were seen in the months of November, December and January, which coincide with the breeding season. Natural markings were unique to individuals and did not change substantially with time, which provided further support for their use in the identification of individual
M. alfredi
over multiple years. Multiple re-sightings of individual
M. alfredi
suggest that many individuals in this population exhibit site fidelity to the examined aggregation sites. As target subsistence fishing for
M. alfredi
exists along the Mozambican coastline, management efforts to monitor and prevent overexploitation at these critical habitats should be a priority.
The reef manta ray
Manta alfredi
aggregates at several sites along the east coast of Australia. Photographic identification and mark–recapture methods were used to report on the site affinity, size ...and structure of this population of
M. alfredi
. A total of 716 individuals were identified in 1982–2012, including 636 at Lady Elliot Island (LEI), southern Great Barrier Reef. Over 60 % of individuals identified were resighted at least once during the study period. Multiple resightings within and among years imply a high degree of site affinity by individuals to aggregation sites. One individual was sighted 11 times at LEI over a 30-yr period. The sex ratio of this population was significantly biased towards females (1.2:1 female-to-male ratio), and females were more commonly resighted than males. Robust design population models were used to estimate the population size of the winter aggregation at LEI over a 4-yr period. The models estimated up to 456 (95 % CI 399–535)
M. alfredi
individuals in the population within one winter season and a high annual apparent survival. This study demonstrated that waters around LEI form a key aggregation site for a large portion of the
M. alfredi
population in east Australian waters.
Aberrant Ras/Raf/MEK/ERK signaling is one of the most prevalent oncogenic alterations and confers survival advantage to tumor cells. Inhibition of this pathway can effectively suppress tumor cell ...growth. For example, sorafenib, a multi-kinase inhibitor targeting c-Raf and other oncogenic kinases, has been used clinically for treating advanced liver and kidney tumors, and also has shown efficacy against other malignancies. However, how inhibition of oncogenic signaling by sorafenib and other drugs suppresses tumor cell growth remains unclear. In this study, we found that sorafenib kills cancer cells by activating PUMA (p53-upregulated modulator of apoptosis), a p53 target and a BH3-only Bcl-2 family protein. Sorafenib treatment induces PUMA in a variety of cancer cells irrespective of their p53 status. Surprisingly, the induction of PUMA by sorafenib is mediated by IκB-independent activation of nuclear factor (NF)-κB, which directly binds to the PUMA promoter to activate its transcription. NF-κB activation by sorafenib requires glycogen synthase kinase 3β activation, subsequent to ERK inhibition. Deficiency in PUMA abrogates sorafenib-induced apoptosis and caspase activation, and renders sorafenib resistance in colony formation and xenograft tumor assays. Furthermore, the chemosensitization effect of sorafenib is dependent on PUMA, and involves concurrent PUMA induction through different pathways. BH3 mimetics potentiate the anti-cancer effects of sorafenib, and restore sorafenib sensitivity in resistant cells. Together, these results demonstrate a key role of PUMA-dependent apoptosis in therapeutic inhibition of Ras/Raf/MEK/ERK signaling. They provide a rationale for manipulating the apoptotic machinery to improve sensitivity and overcome resistance to the therapies that target oncogenic kinase signaling.
Tumor necrosis factor- alpha (TNF- alpha ) is a cytokine that has an important role in immunity and inflammation by inducing cellular responses such as apoptosis. The transcription factor nuclear ...factor- Kappa B (NF- Kappa B) can paradoxically suppress and promote apoptosis in response to TNF- alpha . In this study, we found that p53 upregulated modulator of apoptosis (PUMA), a p53 downstream target and a BH3-only Bcl-2 family member, is directly regulated by NF- Kappa B in response to TNF- alpha . TNF- alpha treatment led to increases in PUMA mRNA and protein levels in human colon cancer cells. The induction of PUMA was p53 independent, and mediated by the p65 component of NF- Kappa B through a Kappa B site in the PUMA promoter. The apoptotic effect of PUMA induction by TNF- alpha was unmasked by depleting the antiapoptotic protein Bcl-X sub(L). In mice, PUMA was also induced by TNF- alpha in an NF- Kappa B-dependent manner. TNF- alpha -induced apoptosis in a variety of tissues and cell types, including small intestinal epithelial cells, hepatocytes, and thymocytes, was markedly reduced in PUMA-deficient mice. Collectively, these results demonstrated that PUMA is a direct target of NF- Kappa B and mediates TNF- alpha -induced apoptosis in vitro and in vivo.Cell Death and Differentiation (2009) 16, 1192-1202; doi:10.1038/cdd.2009.51; published online 15 May 2009
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.
Sustainable exploitation of fisheries populations is challenging to achieve when the size of the population prior to exploitation and the actual numbers removed over time and across fishing zones are ...not clearly known. Quantitative fisheries' modeling is able to address this problem, but accurate and reliable model outcomes depend on high quality input data. Much of this information is obtained through the operation of the fishery under consideration, but while this seems appropriate, biases may occur. For example, poorly quantified changes in fishing methods that increase catch rates can erroneously suggest that the overall population size is increasing. Hence, the incorporation of estimates of abundance derived from independent data sources is preferable. We review and evaluate a fisheries‐independent method of indexing population size; inferring adult abundance from estimates of the genetic effective size of a population (Ne). Recent studies of elasmobranch species have shown correspondence between Ne and ecologically determined estimates of the population size (N). Simulation studies have flagged the possibility that the range of Ne/N ratios across species may be more restricted than previously thought, and also show that declines in Ne track declines in the abundance of model fisheries species. These key developments bring this new technology closer to implementation in fisheries science, particularly for data‐poor fisheries or species of conservation interest.
Predators play a crucial role in the structure and function of ecosystems. However, the magnitude of this role is often unclear, particularly for large marine predators, as predation rates are ...difficult to measure directly. If relevant biotic and abiotic parameters can be obtained, then bioenergetics modelling offers an alternative approach to estimating predation rates, and can provide new insights into ecological processes. We integrate demographic and ecological data for a marine apex predator, the broadnose sevengill shark Notorynchus cepedianus, with energetics data from the literature, to construct a bioenergetics model to quantify predation rates on key fisheries species in Norfolk Bay, Australia. We account for the uncertainty in model parameters by incorporating parameter confidence through Monte Carlo simulations and running alternative variants of the model. Model and parameter variants provide alternative estimates of predation rates. Our simplest model estimates that ca. 1130 ± 137 N. cepedianus individuals consume 11,379 (95% CI: 11,111-11,648) gummy sharks Mustelus antarcticus (~21 tonnes) over a 36-week period in Norfolk Bay, which represents a considerable contribution to total predation mortality on this key fishery species. This study demonstrates how the integration of ecology and fisheries science can provide information for ecosystem and fisheries management.
Inter-specific genetic relationships among regional populations of two species of grouper (
Plectropomus maculatus and
Plectropomus leopardus) were examined using mitochondrial and nuclear markers. ...mtDNA revealed contrasting regional inter-specific patterns whilst nuclear markers revealed contrasting patterns among markers, irrespective of region. In eastern Australia (EA) the species form a single mtDNA lineage, but the two species are reciprocally monophyletic in Western Australia (WA). This supports previous evidence for hybridisation between these species on the east coast. WA
P. leopardus forms a sister relationship with the EA
P. leopardus-maculatus clade while WA
P. maculatus is more basal and sister to the
P. leopardus lineages, indicating mtDNA does not suffer from incomplete lineage sorting for these species. In contrast, one of three nuclear markers (locus 7-90TG) differentiated the species into two reciprocally monophyletic clades, with no evidence of hybridisation or ancestral polymorphism. The remaining two nuclear markers (2-22 and ETS-2) did not separate these two species, while distinguishing other plectropomid species, suggesting incomplete lineage sorting at these nuclear loci. These results together with coalescence analyses suggest that
P. leopardus females have hybridised historically with
P. maculatus males and that
P. maculatus mitochondria were displaced through introgressive hybridisation and fixation in the
P. maculatus founder population on the Great Barrier Reef. The contrasting regional patterns of mtDNA structure may be attributed to Quaternary sea-level changes and shelf width differences driving different reef configurations on each coast. These reef configurations have provided opportunities for local scale interaction and reproduction among species on the narrower EA continental shelves, but not on the broader WA continental shelves.
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