Deep-reef fish communities of the Great Barrier Reef shelf-break: trophic structure and habitat associations

The ecology of habitats along the Great Barrier Reef (GBR) shelf-break has rarely been investigated. Thus, there is little understanding of how associated fishes interact with deeper environments. We examined relationships between deep-reef fish communities and benthic habitat structure. We sampled 48 sites over a large depth gradient (54–260 m) in the central GBR using Baited Remote Underwater Video Stations and multibeam sonar. Fish community composition differed both among multiple shelf-break reefs and habitats within reefs. Epibenthic cover decreased with depth. Deep epibenthic cover included sponges, corals, and macro-algae, with macro-algae present to 194 m. Structural complexity decreased with depth, with more calcified reef, boulders, and bedrock in shallower depths. Deeper sites were flatter and more homogeneous with softer substratum. Habitats were variable within depth strata and were reflected in different fish assemblages among sites and among locations. Overall, fish trophic groups changed with depth and included generalist and benthic carnivores, piscivores, and planktivores while herbivores were rare below 50 m. While depth influenced where trophic groups occurred, site orientation and habitat morphology determined the composition of trophic groups within depths. Future conservation strategies will need to consider the vulnerability of taxa with narrow distributions and habitat requirements in unique shelf-break environments

“Tales and Adventures”: G.A. Henty’s Union Jack and the Competitive World of Publishing for Boys in the 1880s’

In the competitive publishing environment of the late nineteenth century, writers and magazines had to distinguish themselves carefully from potential rivals. This article examines how G.A. Henty’s quality boys’ weekly, Union Jack (1880-83), attempted to secure a niche in the juvenile publishing market by deliberately distinguishing itself from other papers as a literary, imperialist and “healthy” publication. The article explores the design and marketing techniques of the magazine, its status as a fiction paper, the high calibre of its contributors, and its aggressive rhetoric in targeting an exclusively masculine audience. It argues that while Union Jack was marketed as a niche publication, it eventually failed to distinguish itself sufficiently to survive in an extremely competitive environment

An Exact Algorithm for Side-Chain Placement in Protein Design

Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial side-chain placement problem consists of choosing a side-chain placement for each residue position such that the resulting overall energy is minimum. The choice of the side-chain then also determines the amino acid for this position. Many algorithms for this NP-hard problem have been proposed in the context of homology modeling, which, however, reach their limits when faced with large protein design instances. In this paper, we propose a new exact method for the side-chain placement problem that works well even for large instance sizes as they appear in protein design. Our main contribution is a dedicated branch-and-bound algorithm that combines tight upper and lower bounds resulting from a novel Lagrangian relaxation approach for side-chain placement. Our experimental results show that our method outperforms alternative state-of-the art exact approaches and makes it possible to optimally solve large protein design instances routinely

Larval dispersal in a changing ocean with an emphasis on upwelling regions

Dispersal of benthic species in the sea is mediated primarily through small, vulnerable larvae that must survive minutes to months as members of the plankton community while being transported by strong, dynamic currents. As climate change alters ocean conditions, the dispersal of these larvae will be affected, with pervasive ecological and evolutionary consequences. We review the impacts of oceanic changes on larval transport, physiology, and behavior. We then discuss the implications for population connectivity and recruitment and evaluate life history strategies that will affect susceptibility to the effects of climate change on their dispersal patterns, with implications for understanding selective regimes in a future ocean. We find that physical oceanographic changes will impact dispersal by transporting larvae in different directions or inhibiting their movements while changing environmental factors, such as temperature, pH, salinity, oxygen, ultraviolet radiation, and turbidity, will affect the survival of larvae and alter their behavior. Reduced dispersal distance may make local adaptation more likely in well-connected populations with high genetic variation while reduced dispersal success will lower recruitment with implications for fishery stocks. Increased dispersal may spur adaptation by increasing genetic diversity among previously disconnected populations as well as increasing the likelihood of range expansions. We hypothesize that species with planktotrophic (feeding), calcifying, or weakly swimming larvae with specialized adult habitats will be most affected by climate change. We also propose that the adaptive value of retentive larval behaviors may decrease where transport trajectories follow changing climate envelopes and increase where transport trajectories drive larvae toward increasingly unsuitable conditions. Our holistic framework, combined with knowledge of regional ocean conditions and larval traits, can be used to produce powerful predictions of expected impacts on larval dispersal as well as the consequences for connectivity, range expansion, or recruitment. Based on our findings, we recommend that future studies take a holistic view of dispersal incorporating biological and oceanographic impacts of climate change rather than solely focusing on oceanography or physiology. Genetic and paleontological techniques can be used to examine evolutionary impacts of altered dispersal in a future ocean, while museum collections and expedition records can inform modern-day range shifts

Safe and complete contig assembly via omnitigs

Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from $G$ as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201

Investigation of the causes of mass fish kills in the Menindee Region NSW over the summer of 2018–2019

On 15 December 2018 tens of thousands of dead fish were reported along a 30 km stretch of the Darling River near the town of Menindee in New South Wales. High numbers of dead fish were seen in the vicinity of the Old Menindee Weir and Menindee Pump Station. A second, larger fish kill event involving hundreds of thousands of fish was reported on 6 January 2019 on the same stretch of river. A third event followed on 28 January, killing millions of fish. Members of the panel witnessed the beginnings of a fourth event on 4 February 2019. Many different sectors of Australian society, and of the Menindee region itself, are distressed knowing that fish have been dying en masse, and are concerned about the implications for the health of the river. In addition, these fish are of high cultural significance to Indigenous communities in the region, including those holding Native Title rights. In response to the first two kills, the Academy was requested by the Leader of the Opposition, the Hon. Bill Shorten MP to provide advice on the immediate causes, as well as exacerbating circumstances from water diversions, agricultural runoff or climate change, and to provide recommendations.Australian Academy of Science, Expert Panel: Craig Moritz, Linda Blackall, Jenny Davis, Tim Flannery, Lee Godden, Lesley Head, Sue Jackson, Richard Kingsford, Sarah Wheeler, John William

A combinatorial optimization approach for diverse motif finding applications

BACKGROUND: Discovering approximately repeated patterns, or motifs, in biological sequences is an important and widely-studied problem in computational molecular biology. Most frequently, motif finding applications arise when identifying shared regulatory signals within DNA sequences or shared functional and structural elements within protein sequences. Due to the diversity of contexts in which motif finding is applied, several variations of the problem are commonly studied. RESULTS: We introduce a versatile combinatorial optimization framework for motif finding that couples graph pruning techniques with a novel integer linear programming formulation. Our approach is flexible and robust enough to model several variants of the motif finding problem, including those incorporating substitution matrices and phylogenetic distances. Additionally, we give an approach for determining statistical significance of uncovered motifs. In testing on numerous DNA and protein datasets, we demonstrate that our approach typically identifies statistically significant motifs corresponding to either known motifs or other motifs of high conservation. Moreover, in most cases, our approach finds provably optimal solutions to the underlying optimization problem. CONCLUSION: Our results demonstrate that a combined graph theoretic and mathematical programming approach can be the basis for effective and powerful techniques for diverse motif finding applications

Network Archaeology: Uncovering Ancient Networks from Present-day Interactions

Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been limited by the unavailability of past versions of networks. To overcome these limitations, we propose several algorithms for reconstructing a network's history of growth given only the network as it exists today and a generative model by which the network is believed to have evolved. Our likelihood-based method finds a probable previous state of the network by reversing the forward growth model. This approach retains node identities so that the history of individual nodes can be tracked. We apply these algorithms to uncover older, non-extant biological and social networks believed to have grown via several models, including duplication-mutation with complementarity, forest fire, and preferential attachment. Through experiments on both synthetic and real-world data, we find that our algorithms can estimate node arrival times, identify anchor nodes from which new nodes copy links, and can reveal significant features of networks that have long since disappeared.Comment: 16 pages, 10 figure

A Novel Method of Characterizing Genetic Sequences: Genome Space with Biological Distance and Applications

Most existing methods for phylogenetic analysis involve developing an evolutionary model and then using some type of computational algorithm to perform multiple sequence alignment. There are two problems with this approach: (1) different evolutionary models can lead to different results, and (2) the computation time required for multiple alignments makes it impossible to analyse the phylogeny of a whole genome. This motivates us to create a new approach to characterize genetic sequences.To each DNA sequence, we associate a natural vector based on the distributions of nucleotides. This produces a one-to-one correspondence between the DNA sequence and its natural vector. We define the distance between two DNA sequences to be the distance between their associated natural vectors. This creates a genome space with a biological distance which makes global comparison of genomes with same topology possible. We use our proposed method to analyze the genomes of the new influenza A (H1N1) virus, human rhinoviruses (HRV) and mammalian mitochondrial. The result shows that a triple-reassortant swine virus circulating in North America and the Eurasian swine virus belong to the lineage of the influenza A (H1N1) virus. For the HRV and mammalian mitochondrial genomes, the results coincide with biologists' analyses.Our approach provides a powerful new tool for analyzing and annotating genomes and their phylogenetic relationships. Whole or partial genomes can be handled more easily and more quickly than using multiple alignment methods. Once a genome space has been constructed, it can be stored in a database. There is no need to reconstruct the genome space for subsequent applications, whereas in multiple alignment methods, realignment is needed to add new sequences. Furthermore, one can make a global comparison of all genomes simultaneously, which no other existing method can achieve