Bree J. Tillett

NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data.

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.

A review of the application of molecular genetics for fisheries management and conservation of sharks and rays

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.

Evidence for reproductive philopatry in the bull shark Carcharhinus leucas

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.

Similar life history traits in bull (Carcharhinus leucas) and pig-eye (C. amboinensis) sharks

Appropriate management strategies for coastal regions require an understanding of how ecological similari- ties 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 asymptoticlength(LN)(� s.e.)wasestimatedtobe2672(� 11.94)mmwithagrowthcoefficient(k)of0.145year � 1 .Male pig-eye sharks matured slightly earlier than females (12 years) and survived.26 years. Theoretical asymptotic length for males (LN )( � s.e.) was also smaller (2540 � 13.056)mm and they grew faster (k ¼0.161year � 1 ) than females. Bull sharks matured at 9.5 years and reached a maximum theoretical size (LN )( � s.e.) of 3119mm (� 9.803) with a similar growth coefficient (k ¼0.158 year � 1 ) 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.

A short work-flow to effectively source faecal pollution in recreational waters – A case study

Microbial pollution of recreational waters poses a significant public health risk which, unless mitigated, will continue to increase with population growth. Water managers must implement strategies to accurately discriminate and source human from animal faecal contamination in complex urbanised environments. Our case-study used a new combination of chemical (i.e. ammonia) and microbial (i.e. Escherichia coli, Bacteroides spp.) faecal monitoring tools in a targeted multi-tiered approach to quickly identify pollution hot-spots and track high-risk subterranean stormwater drains in real-time. We successfully located three point sources of human faecal pollution (both episodic and constant pollution streams) within 11 catchments in a total monitoring time of four months. Alternative approaches for obtaining such fine-scale accuracy are typically labour intensive and require expensive equipment.