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

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.

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

We compare vertebral microchemistry with previously described age-related movement patterns of bull sharks Carcharhinus leucas and pig-eye sharks C. amboinensis within coastal waters of north Australia. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) quantified the chemical signatures of nursery habitats within the vertebrae of juvenile and adult sharks. We examined evidence for adults returning to these habitats by applying LA-ICP-MS along a growth axis of their vertebrae. We transposed chemical signatures with growth increments in adult vertebrae to correlate with age estimates. Unique elemental signatures were identified in each of the freshwater nurseries, but we did not find them in adult vertebrae. Age-specific changes in vertebral microchemistry in mature female bull sharks correlate with periodic returns every 1 to 2 yr to less saline environments to pup. We were unable to discriminate among natal habitats of pig-eye sharks using elemental fingerprints, and age-specific changes in vertebral microchemistry were also absent. We conclude that changes in vertebral microchemistry correlate with known habitat use patterns of the bull and pig-eye sharks, showing the potential of vertebral microchemistry to discern movement patterns in sharks. KEY WORDS: Vertebral microchemistry · LA-ICP-MS · Movement · Long-term · Resource partitioning · CarcharhinidaeResale or republication not permitted without written consent of the publisher Mar Ecol Prog Ser 434: 133-142, 2011 Speed et al. 2010) that are critical to the maintenance of genetic diversity and replenishment of populations (Hueter et al. 2005).Studies tracking shark movements and identifying patterns of habitat use in coastal regions typically involve tagging with standard (numerical), satellite or sonar tags (Speed et al. 2010). Such an approach is often logistically difficult and expensive because it first involves the capture, tagging and release (in good condition) of the shark. Furthermore, the animals must either be recaptured (standard tags), or tags must report to satellites or arrays of listening stations (sonar tags) for data acquisition (Voegeli et al. 2001, Simpfendorfer & Heupel 2004. Rates of recapture are usually low, while failure of expensive satellite tags to report is commonplace (Hays et al. 2007). Arrays of listening stations require considerable effort to deploy, download and maintain, which can limit the duration and spatial extent of a study using this approach. Despite these problems, studies using these techniques have mapped fine-scale (25 km) movements of different-age cohorts of sharks in shallow coastal waters (Simpfendorfer et al. 2005, Yeiser et al. 2008, Heithaus et al. 2009, Ortega et al. 2009, but the logistics, cost and limited life span of tags have restricted the number of target individuals and species and, in the case of sonar tags, the spatial extent of the sampling area.To overcome the limitations associated with conventional tracking, natural chemical fingerprints are a developing ...

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Background Short-chain fatty acids (SCFAs) produced by the gut microbiota have beneficial anti-inflammatory and gut homeostasis effects and prevent type 1 diabetes (T1D) in mice. Reduced SCFA production indicates a loss of beneficial bacteria, commonly associated with chronic autoimmune and inflammatory diseases, including T1D and type 2 diabetes. Here, we addressed whether a metabolite-based dietary supplement has an impact on humans with T1D. We conducted a single-arm pilot-and-feasibility trial with high-amylose maize-resistant starch modified with acetate and butyrate (HAMSAB) to assess safety, while monitoring changes in the gut microbiota in alignment with modulation of the immune system status. Results HAMSAB supplement was administered for 6 weeks with follow-up at 12 weeks in adults with long-standing T1D. Increased concentrations of SCFA acetate, propionate, and butyrate in stools and plasma were in concert with a shift in the composition and function of the gut microbiota. While glucose control and insulin requirements did not change, subjects with the highest SCFA concentrations exhibited the best glycemic control. Bifidobacterium longum, Bifidobacterium adolescentis, and vitamin B7 production correlated with lower HbA1c and basal insulin requirements. Circulating B and T cells developed a more regulatory phenotype post-intervention. Conclusion Changes in gut microbiota composition, function, and immune profile following 6 weeks of HAMSAB supplementation were associated with increased SCFAs in stools and plasma. The persistence of these effects suggests that targeting dietary SCFAs may be a mechanism to alter immune profiles, promote immune tolerance, and improve glycemic control for the treatment of T1D. Trial registration ACTRN12618001391268. Registered 20 August 2018,https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=375792

Appropriate management strategies for coastal regions require an understanding of how ecological similarities and differences among species shape ecosystem processes. Here, we tested whether morphological similarity equated to similar age and growth patterns in two common coastal sharks in northern Australia. Vertebrae of 199 pig-eye (Carcharhinus amboinensis) and 94 bull (C. leucas) sharks were sourced principally from commercial fisheries operating along the Northern Territory coastline during 2007-2009. We sectioned vertebrae to provide estimates of age of these animals. Model averaging results indicated female pig-eye sharks matured at 13 years and lived .30 years. Theoretical asymptotic length (L N ) (AEs.e.) was estimated to be 2672 (AE11.94) mm with a growth coefficient (k) of 0.145 year À1 . Male pig-eye sharks matured slightly earlier than females (12 years) and survived .26 years. Theoretical asymptotic length for males (L N ) (AEs.e.) was also smaller (2540 AE 13.056) mm and they grew faster (k ¼ 0.161 year À1 ) than females. Bull sharks matured at 9.5 years and reached a maximum theoretical size (L N ) (AEs.e.) of 3119 mm (AE9.803) with a similar growth coefficient (k ¼ 0.158 year À1 ) to pig-eye sharks. Longevity of bull sharks was estimated to be more than 27 years. Our results indicate that these patterns of high longevity and slow growth are indicative of low resilience and high susceptibility to over-exploitation of these coastal sharks.

Glyphis sharks and pristid sawfishes are globally threatened. While some populations still exist in northern Australia, their distributions are poorly quantified. We used catch records from commercial fisheries and independent surveys to estimate the broad distribution and relative abundances of 2 Glyphis sharks (G. glyphis and G. garricki) and 4 pristid sawfishes (Pristis pristis, P. zijsron, P. clavata and Anoxypristis cuspidata) along the coast, estuaries and river systems of the Northern Territory, Australia. Coarse-scale catch data and records from commercial fishing logbooks that report encounters with Threatened, Endangered and Protected species confirm that small, fragmented populations are distributed across the Northern Territory coastline and suggest limited fishery interactions, although underreporting might occur.KEY WORDS: Sharks · Habitat · Fishing · Conservation · Management · Pristis spp. · Anoxypristis spp. Resale or republication not permitted without written consent of the publisherEndang Species Res 21: [171][172][173][174][175][176][177][178][179][180] 2013 tions, thus hindering conservation planning (IUCN 2010). Two species of Glyphis sharks have been described in northern Australia, G. glyphis (the speartooth shark, previously known as Glyphis sp. A) and G. garricki (the northern river shark, previously known as Glyphis sp. C) (Larson 2002, Martin 2005, Peverell et al. 2006, Compagno et al. 2008, Wynen et al. 2009). Both species have restricted distributions; G. glyphis has only been recorded in the Northern Territory (Adelaide River, East, South and West Alligator Rivers, Murganella Creek and Marrakai Creek) and in Queensland (Wenlock and Ducie Rivers, Port Musgrave and the Bizant River) (Peverell et al. 2006, Compagno et al. 2008. The only other record of this species globally is from Papua New Guinea (Compagno et al. 2008). G. garricki is also found in Australia in the Northern Territory (Adelaide, East and South Alligator and Mary Rivers) but unlike G. glyphis, it has also been recorded in Western Australia (King Sound in the Kimberley region) (Taniuchi et al. 1991, Thorburn & Morgan 2004. Similar to G. glyphis, the only other place where this species has been recorded is Papua New Guinea (Taniuchi et al. 1991, Compagno et al. 2008. Both Glyphis spp. are considered extremely rare, although no population estimates are available for either species. G. glyphis and G. garricki are currently listed as Critically Endangered in the IUCN Red List (www. iucn redlist .org), and critically endangered and endangered under the Australian Commonwealth Environment Protection and Biodiversity Conservation (EPBC) Act 1999, respectively. Due to these classifications, both species are identified as 'key' species for conservation planning (National Oceans Office 2004).There are 4 sawfishes in Australia: the freshwater sawfish Pristis pristis (previously known as P. microdon), green sawfish P. zijsron, dwarf sawfish P. clavata and narrow sawfish Anoxypristis cuspidata (Thorburn et al. 2003, ...