Whole-genome shotgun sequence assembly enables rapid gene characterization in the tropical fish barramundi, Lates calcarifer

[Extract] Source description: Barramundi, Lates calcarifer, is a commercially important fish farmed throughout Australia and South-East Asia. Despite an increasing availability of genetic resources for the species (e.g. microsatellite and SNP markers, linkage and BAC-based maps and transcriptomic assemblies), the complete characterization of genes is still reliant on laborious molecular methods (e.g. genome walking/RACE PCR cloning/Sanger sequencing)

Influence of drainage divides versus arid corridors on genetic structure and demography of a widespread freshwater turtle, Emydura macquarii krefftii, from Australia

The influence of Pleistocene climatic cycles on Southern Hemisphere biotas is not yet well understood. Australia's eastern coastal margin provides an ideal setting for examining the relative influence of landscape development, sea level fluctuation, and cyclic climatic aridity on the evolution of freshwater biodiversity. We examined the impact of climatic oscillations and physical biogeographic barriers on the evolutionary history of the wide-ranging Krefft's river turtle (Emydura macquarii krefftii), using range-wide sampling (649 individuals representing 18 locations across 11 drainages) and analysis of mitochondrial sequences (similar to 1.3-kb control region and ND4) and nuclear microsatellites (12 polymorphic loci). A range of phylogeographic (haplotype networks, molecular dating), demographic (neutrality tests, mismatch distributions), and population genetic analyses (pairwise F-ST, analysis of molecular variance, Bayesian clustering analysis) were implemented to differentiate between competing demographic (local persistence vs. range expansion) and biogeographic (arid corridor vs. drainage divide) scenarios. Genetic data reveal population genetic structure in Krefft's river turtles primarily reflects isolation across drainage divides. Striking north-south regional divergence (2.2% ND4 p-distance; c. 4.73Ma, 95% higher posterior density (HPD) 2.08-8.16Ma) was consistent with long-term isolation across a major drainage divide, not an adjacent arid corridor. Ancient divergence among regional lineages implies persistence of northern Krefft's populations despite the recurrent phases of severe local aridity, but with very low contemporary genetic diversity. Stable demography and high levels of genetic diversity are inferred for southern populations, where aridity was less extreme. Range-wide genetic structure in Krefft's river turtles reflects contemporary and historical drainage architecture, although regional differences in the extent of Plio-Pleistocene climatic aridity may be reflected in current levels of genetic diversity

Solar flares and their associated processes

The evolution of the solar neutrino flux which is described by the wave function $\Psi^T=(\nu_{eL},\nu_{XL}, \overline{\nu}_{eL}, \overline{\nu}_{XL})$ is examined. Our treatment of the problem holds for any standard model (SM) extensions possessing nonzero dipole magnetic and anapole moments. When the solar neutrino flux moves through the solar flare (SF) region in the preflare period, then it undergoes the additional (compared with the SM) resonance conversions. As a result, the weakening the electron neutrinos flux takes place. On the other hand, existence of the additional resonances lead to appearance of the $\overline{\nu}_{eL}$ and $\overline{\nu}_{XL}$ neutrinos that could be detected by the terrestrial detectors. The hypothesis of the $\nu_e$-induced $\beta$-decays is also discussed. According to it, before the large SF, decreasing the $\beta$-decay rate for some elements takes place. The possible influence of the electron antineutrino flux produced in the superflares on the regime of the hypothetical georeactor is considered.Comment: 11 pages. arXiv admin note: text overlap with arXiv:hep-ph/0401221 by other author

Genetic Detection and a Method to Study the Ecology of Deadly Cubozoan Jellyfish

Cubozoan jellyfish pose a risk of envenomation to humans and a threat to many businesses, yet crucial gaps exist in determining threats to stakeholders and understanding their ecology. Environmental DNA (eDNA) provides a cost-effective method for detection that is less labour intensive and provides a higher probability of detection. The objective of this study was to develop, optimise and trial the use of eDNA to detect the Australian box jellyfish, Chironex fleckeri. This species was the focus of this study as it is known to have the strongest venom of any cubozoan; it is responsible for more than 200 recorded deaths in the Indo-Pacific region. Further, its ecology is poorly known. Herein, a specific and sensitive probe-based assay, multiplexed with an endogenous control assay, was developed, and successfully utilised to detect the deadly jellyfish species and differentiate them from closely related taxa. A rapid eDNA decay rate of greater than 99% within 27 h was found with no detectable influence from temperature. The robustness of the technique indicates that it will be of high utility for detection and to address knowledge gaps in the ecology of C. fleckeri; further, it has broad applicability to other types of zooplankton

Brain-Computer Interfaces in Medicine

Brain-computer interfaces (BCIs) acquire brain signals, analyze them, and translate them into commands that are relayed to output devices that carry out desired actions. BCIs do not use normal neuromuscular output pathways. The main goal of BCI is to replace or restore useful function to people disabled by neuromuscular disorders such as amyotrophic lateral sclerosis, cerebral palsy, stroke, or spinal cord injury. From initial demonstrations of electroenceph-alography-based spelling and single-neuron-based device control, researchers have gone on to use electroenceph-alographic, intracortical, electrocorticographic, and other brain signals for increasingly complex control of cursors, robotic arms, prostheses, wheelchairs, and other devices. Brain-computer interfaces may also prove useful for rehabilitation after stroke and for other disorders. In the future, they might augment the performance of surgeons or other medical professionals. Brain-computer interface technology is the focus of a rapidly growing research and development enterprise that is greatly exciting scientists, engineers, clinicians, and the public in general. Its future achievements will depend on advances in 3 crucial areas. Brain-computer interfaces need signal-acquisition hardware that is convenient, portable, safe, and able to function in all environments. Brain-computer interface systems need to be validated in long-term studies of real-world use by people with severe disabilities, and effective and viable models for their widespread dissemination must be implemented. Finally, the day-to-day and moment-to-moment reliability of BCI performance must be improved so that it approaches the reliability of natural muscle-based function

Gene flow and genetic structure in Nile perch, Lates niloticus, from African freshwater rivers and lakes

Background Geological evolution of the African continent has been subject to complex processes including uplift, volcanism, desert formation and tectonic rifting. This complex geology has created substantial biogeographical barriers, and coupled with anthropogenic introductions of freshwater fishes, has influenced the genetic diversity, connectivity and sub-structuring of the teleost fauna. Nile perch, Lates niloticus, is an iconic fish in Africa and is of high commercial importance, both in the species' native range and where it has been translocated. However, the species is in decline and there is a need to understand its population genetic structure to facilitate sustainable management of the fishery and aquaculture development. Methodology Nile perch tissue samples were acquired from two West and four East (Lakes; Albert, Kyoga, Victoria and Turkana) African locations. Nineteen polymorphic microsatellite loci were used to study the genetic variation among populations across regions (West and East Africa), as well as between native and introduced environments within East Africa. Principal findings and their significance Results revealed strong and significant genetic structuring among populations across the sampled distribution (divergence across regions, FCT = 0.26, P = 0.000). STRUCTURE analysis at a broad scale revealed K = 2 clusters, the West African individuals were assigned to one cluster, while all individuals from the East African region, regardless of whether native or introduced, were assigned to another cluster. The distinct genetic clusters identified in the current study between the West and East African Nile perch, appear to have been maintained by presence of biogeographic barriers and restricted gene flow between the two regions. Therefore, any translocations of Nile perch should be carefully considered across the regions of West and East Africa. Further analysis at a regional scale revealed further structuring of up to K = 3 genetic clusters in East African Nile perch. Significantly (P < 0.05) lower genetic diversity based on analysis of allelic richness (AR) was obtained for the two translocated populations of Lake Kyoga (AR = 3.61) and Lake Victoria (AR = 3.52), compared to Nile perch populations from their putative origins of Lakes Albert (AR = 4.12) and Turkana (AR = 4.43). The lower genetic diversity in the translocated populations may be an indication of previous bottlenecks and may also indicate a difficulty for these populations to persist and adapt to climatic changes and anthropogenic pressures that are currently present in the East African region

Genome-wide comparisons reveal evidence for a species complex in the black-lip pearl oyster Pinctada margaritifera (Bivalvia: Pteriidae)

Evolutionary relationships in the black-lip pearl oyster Pinctada margaritifera which is highly valued for pearl production remain poorly understood. This species possesses an 18,000 km Indo-Pacific natural distribution, and its current description includes six subspecies defined exclusively on morphological characters. To evaluate its taxonomic identity using molecular data, 14 populations in both the Indian and Pacific Oceans (n = 69), and the congeneric taxa P. maxima and P. mazatlanica (n = 29 and n = 10, respectively) were sampled. Phylogenomic reconstruction was carried out using both 8,308 genome-wide SNPs and 10,000 dominant loci (DArTseq PAVs). Reconstructions using neighbour-joining (Nei’s 1972 distances), maximum likelihood and Bayesian approaches all indicate that the taxonomy of P. margaritifera is quite complex, with distinct evolutionary significant units (ESUs) identified within Tanzanian and Iranian populations. Contrastingly, phylogenies generated for Pacific Ocean oysters resolved a large monophyletic clade, suggesting little support for two current morphological subspecies classifications. Furthermore, P. mazatlanica formed a basal clade closest to French Polynesian P. margaritifera, suggesting it may be conspecific. Collectively, these findings provide evidence that P. margaritifera comprises a species complex, perhaps as a result of population fragmentation and increased divergence at range limits

Transcriptomic analysis of gill and kidney from Asian seabass (Lates calcarifer) acclimated to different salinities reveals pathways involved with euryhalinity

Asian seabass (or commonly known as barramundi), Lates calcarifer, is a bony euryhaline teleost from the Family Latidae, inhabiting nearshore, estuarine, and marine connected freshwaters throughout the tropical Indo-West Pacific region. The species is catadromous, whereby adults spawn in salinities between 28 and 34 ppt at the mouth of estuaries, with resultant juveniles usually moving into brackish and freshwater systems to mature, before returning to the sea to spawn again as adults. The species lives in both marine and freshwater habitats and can move quickly between the two; thus, the species’ ability to tolerate changes in salinity makes it a good candidate for studying the salinity acclimation response in teleosts. In this study, the transcriptome of two major osmoregulatory organs (gills and kidneys) of young juvenile Asian seabass reared in freshwater and seawater were compared. The euryhaline nature of Asian seabass was found to be highly pliable and the moldability of the trait was further confirmed by histological analyses of gills and kidneys. Differences in major expression pathways were observed, with differentially expressed genes including those related to osmoregulation, tissue/organ morphogenesis, and cell volume regulation as central to the osmo-adaptive response. Additionally, genes coding for mucins were upregulated specifically under saline conditions, whereas several genes important for growth and development, as well as circadian entrainment were specifically enriched in fish reared in freshwater. Routing of the circadian rhythm mediated by salinity changes could be the initial step in salinity acclimation and possibly migration in euryhaline fish species such as the Asian seabas

Epigenetics underpins phenotypic plasticity of protandrous sex change in fish

Abstract Phenotypic plasticity is an important driver of species resilience. Often mediated by epigenetic changes, phenotypic plasticity enables individual genotypes to express variable phenotypes in response to environmental change. Barramundi (Lates calcarifer) are a protandrous (male-first) sequential hermaphrodite that exhibits plasticity in length-at-sex change between geographic regions. This plasticity is likely to be mediated by changes in DNA methylation (DNAm), a well-studied epigenetic modification. To investigate the relationships between length, sex, and DNAm in a sequential hermaphrodite, here, we compare DNAm in four conserved vertebrate sex-determining genes in male and female barramundi of differing lengths from three geographic regions of northern Australia. Barramundi first mature as male and later sex change to female upon the attainment of a larger body size; however, a general pattern of increasing female-specific DNAm markers with increasing length was not observed. Significant differences in DNAm between males and females of similar lengths suggest that female-specific DNAm arises rapidly during sex change, rather than gradually with fish growth. The findings also reveal that region-specific differences in length-at-sex change are accompanied by differences in DNAm and are consistent with variability in remotely sensed sea temperature and salinity. Together, these findings provide the first in situ evidence for epigenetically and environmentally mediated sex change in a protandrous hermaphrodite and offer significant insight into the molecular and ecological processes governing the marked and unique plasticity of sex in fish

Comparison of intestinal bacterial communities in asymptomatic and diseased Asian seabass (Lates calcarifer) with chronic enteritis and mixed bacterial infections

Asian seabass (Lates calcarifer) is a major aquaculture food fish species in Singapore. Farming of this species is increasingly threatened by frequent outbreaks of infectious diseases, resulting in mortality exceeding 50–70%. In this study, we investigated the comparative gut bacterial microbiota using 16S rRNA metasequencing between asymptomatic and diseased juvenile fish collected during a disease outbreak soon after stocking. Mild to severe chronic granulomatous enteritis was observed histopathologically in both asymptomatic and diseased fish. Kidneys of diseased fish tested PCR positive for the ‘big belly’ novel Vibrio spp., Streptococcus iniae and Vibrio harveyi. These bacteria were also readily detected by PCR in water samples corresponding to tanks fish were sampled from. Potentially beneficial microbes that promote gut health such as Firmicutes, Bacteroidota and Actinobacteriota were the dominant phyla in the intestinal microbiota of asymptomatic fish. Moreover, the bacteria with probiotic potential such as Lactobacillus only presented in asymptomatic fish, and Weissella was unique and prevalent (47.59%) in asymptomatic fish during the recovery phase of the disease outbreak, making them candidate biomarkers for monitoring health status of L. calcarifer. Conversely, diseased fish showed reduced diversity of their gut microbiome, with high abundance of members of the phylum Proteobacteria. Vibrio was the most dominant genus (87.3%) and Streptococcus iniae was only detected in diseased fish. These findings provide a baseline study for understanding changes in intestinal microbiota in newly stocked fish with mixed bacterial infection, biomarker assisted health monitoring, and future host-derived probiotics screening in L. calcarifer