Recent advances in next generation sequencing have enhanced the resolution of population genetic studies of non-model organisms through increased marker generation and sample throughput. Using double digest restriction siteassociated DNA sequencing (ddRADseq), we investigated the population structure of the commercially important southern rock lobster, Jasus edwardsii, in Australia and New Zealand with the aim of identifying a panel of SNP markers that could be used to trace country of origin. Four ddRADseq libraries comprising a total of 91 individuals were sequenced on the Illumina MiSeq platform and demultiplexed reads were used to create a reference catalog of loci. Individual reads were then mapped to the reference catalog and variant calling was performed. We have characterized two single nucleotide polymorphism (SNP) panels comprised in total of 656 SNPs. The first panel contained 535 neutral SNPs, and the second, 121 outlier SNPs that were characteristic of being putatively under selection. Both neutral and outlier SNP panels showed significant differentiation between the two countries, with the outlier loci demonstrating much larger FST values (FST outlier SNP panel = 0.134, P < 0.0001; FST neutral SNP panel = 0.022, P < 0.0001). Assignment tests performed with the outlier SNP panel allocated 100% of the individuals to country of origin, demonstrating the usefulness of these markers for food traceability of J. edwardsii.

Biodiversity conservation is a worldwide concern and proper management of threatened species or communities depends on reliable and accurate data collection. Despite the broad utility of environmental DNA (eDNA) for conservation management and the necessity for appropriate biodiversity management in the tropics, eDNA-based research conducted in tropical regions so far comprises only a small proportion of the cumulative eDNA literature. To address the growing demand for rapid and reliable species and community level ecological data in tropical regions, we provide an aquatic eDNA-focused review of (1) challenges and considerations for sampling design and inference of eDNA data in the tropics, and (2) eDNA applications relevant to ecological research and biodiversity management in the tropics. We propose that the collaborative incorporation of eDNA sampling with conventional field surveys harbours the potential to revolutionize the effectiveness of biodiversity conservation management in tropical regions.

Population structure of many marine organisms is spatially patchy and varies within and between years, a phenomenon defined as chaotic genetic patchiness. This results from the combination of planktonic larval dispersal and environmental stochasticity. Additionally, in species with bi-partite life, postsettlement selection can magnify these genetic differences. The high fecundity (up to 500,000 eggs annually) and protracted larval duration (12-24 months) and dispersal of the southern rock lobster, Jasus edwardsii, make it a good test species for chaotic genetic patchiness and selection during early benthic life. Here, we used double digest restriction site-associated DNA sequencing (ddRADseq) to investigate chaotic genetic patchiness and postsettlement selection in this species. We assessed differences in genetic structure and diversity of recently settled pueruli across four settlement years and between two sites in southeast Australia separated by approximately 1,000 km. Postsettlement selection was investigated by identifying loci under putative positive selection between recently settled pueruli and postpueruli and quantifying differences in the magnitude and strength of the selection at each year and site. Genetic differences within and among sites through time in neutral SNP markers indicated chaotic genetic patchiness. Recently settled puerulus at the southernmost site exhibited lower genetic diversity during years of low puerulus catches, further supporting this hypothesis. of spawning (Hendry, Berg, & Quinn, 1999), individual reproductive success (Hedgecock, 1994), pelagic larval duration (PLD) (Palumbi, 1994), larval behaviour (Raimondi & Keough, 1990) and natural selection (Cowen et al., 2000). Variability in the interaction of all those factors means that ephemeral fine-scale genetic heterogeneity or chaotic genetic patchiness could occur rather than the expected homogenous genetic diversity (Johnson & Black, 1982).Selective processes taking place before and after settlement can also lead to temporal genetic variation in the allele frequencies of a population (Johnson & Wernham, 1999). and 24 months in this phase before metamorphosing into a postlarva, known as puerulus (Booth, 1994). Phyllosoma experience up to 98% mortality during their protracted PLD (Lesser, 1978). This is not uncommon in marine invertebrates, and in the case of a sea urchin, although 2% of survivors were found to be sufficient to replenish a population, they carried a smaller representation of the overall genetic diversity of the adult population (Flowers, Schroeter, & Burton, 2002). Once pueruli settle, they remain sedentary and short distance migration is restricted to nocturnal foraging or retreating to protected areas during moulting (George, 2005). Settlement of J. edwardsii pueruli in southeastern Australia ishighest between the months of July and February and peaks during winter months (Gardner, Frusher, Kennedy, & Cawthorn, 2001).Puerulus settlement has been monitored in southeastern Australia for the past four d...

Halophytes, such as seagrasses, predominantly form habitats in coastal and estuarine areas. These habitats can be seasonally exposed to hypo-salinity events during watershed runoff exposing them to dramatic salinity shifts and osmotic shock. The manifestation of this osmotic shock on seagrass morphology and phenology was tested in three Indo-Pacific seagrass species, Halophila ovalis, Halodule uninervis and Zostera muelleri, to hypo-salinity ranging from 3 to 36 PSU at 3 PSU increments for 10 weeks. All three species had broad salinity tolerance but demonstrated a moderate hypo-salinity stress response – analogous to a stress induced morphometric response (SIMR). Shoot proliferation occurred at salinities <30 PSU, with the largest increases, up to 400% increase in shoot density, occurring at the sub-lethal salinities <15 PSU, with the specific salinity associated with peak shoot density being variable among species. Resources were not diverted away from leaf growth or shoot development to support the new shoot production. However, at sub-lethal salinities where shoots proliferated, flowering was severely reduced for H. ovalis, the only species to flower during this experiment, demonstrating a diversion of resources away from sexual reproduction to support the investment in new shoots. This SIMR response preceded mortality, which occurred at 3 PSU for H. ovalis and 6 PSU for H. uninervis, while complete mortality was not reached for Z. muelleri. This is the first study to identify a SIMR in seagrasses, being detectable due to the fine resolution of salinity treatments tested. The detection of SIMR demonstrates the need for caution in interpreting in-situ changes in shoot density as shoot proliferation could be interpreted as a healthy or positive plant response to environmental conditions, when in fact it could signal pre-mortality stress.