Bio-physical determinants of sediment accumulation on an offshore coral reef: A snapshot study

Sediments are found on all coral reefs around the globe. However, the amount of sediment in different reservoirs, and the rates at which sediments move between reservoirs, can shape the biological functioning of coral reefs. Unfortunately, relatively few studies have examined reef sediment dynamics, and associated bio-physical drivers, simultaneously over matching spatial and temporal scales. This has led to a partial understanding of how sediments and living reef systems are connected, especially on clear-water offshore reefs. To address this problem, four sediment reservoirs/sedimentary processes and three bio-physical drivers were quantified across seven different reef habitats/depths at Lizard Island, an exposed mid-shelf reef on the Great Barrier Reef. Even in this clear-water reef location a substantial load of suspended sediment passed over the reef; a load theoretically capable of replacing the entire standing stock of on-reef turf sediments in just 8 h. However, quantification of actual sediment deposition suggested that just 2 % of this passing sediment settled on the reef. The data also revealed marked spatial incongruence in sediment deposition (sediment trap data) and accumulation (TurfPod data) across the reef profile, with the flat and back reef emerging as key areas of both deposition and accumulation. By contrast, the shallow windward reef crest was an area of deposition but had a limited capacity for sediment accumulation. These cross-reef patterns related to wave energy and reef geomorphology, with low sediment accumulation on the ecologically important reef crest aligning with substantial wave energy. These findings reveal a disconnect between patterns of sediment deposition and accumulation on the benthos, with the ‘post-settlement’ fate of sediments dependent on local hydrodynamic conditions. From an ecological perspective, the data suggests key contextual constraints (wave energy and reef geomorphology) may predispose some reefs or reef areas to high-load turf sediment regimes

Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100)

MAGIS-100 is a next-generation quantum sensor under construction at Fermilab that aims to explore fundamental physics with atom interferometry over a 100-meter baseline. This novel detector will search for ultralight dark matter, test quantum mechanics in new regimes, and serve as a technology pathfinder for future gravitational wave detectors in a previously unexplored frequency band. It combines techniques demonstrated in state-of-the-art 10-meter-scale atom interferometers with the latest technological advances of the world's best atomic clocks. MAGIS-100 will provide a development platform for a future kilometer-scale detector that would be sufficiently sensitive to detect gravitational waves from known sources. Here we present the science case for the MAGIS concept, review the operating principles of the detector, describe the instrument design, and study the detector systematics.Comment: 65 pages, 18 figure

Within and across flock genetic relationships for breech flystrike resistance indicator traits

Introduction: • Breech fly strike is a major problem - Mulesing has been used as a control method - Being phased out due to welfare concerns • Breeding for resistance through indicator traits - Wrinkle, wool cover and colour, dags and fleece rot • Require correlations between indicator and production traits • Across v within flock effects also an issue ... Importance of Visual Traits: • Main goal to increase breech strike resistance • Other goals - Easy care sheep - Reduced urine stain - Reduced crutching - Reduced reliance on chemicals - Improved wool qualit

Optimised Livestock Breeding Programs Using Female Reproductive Technologies and Genomic Selection

This thesis explores various methods to optimise breeding programs that use female reproductive technologies and genomic selection. Simulation studies have shown that female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro embryo production and transfer (JIVET) can increase rates of genetic gain through increased female selection intensity and decreased generation interval. Furthermore the use of genomic selection has facilitated better selection decisions to be made on younger selection candidates that may not have phenotypic measurements. When combining genomic selection with reproductive technologies the rate of genetic gain could be further accelerated. However intensive use of the best females in breeding programs can also increase the rate of inbreeding to unsustainable levels. This thesis aimed to stochastically simulate breeding programs where reproductive and genomic technologies are optimally implemented while maintaining a sustainable increase of inbreeding. The impacts of using reproductive technologies and/or genomic selection were evaluated for breeding programs across species. Furthermore, the thesis investigated a cost-benefit analysis of using reproductive technologies which led to a further study that optimized the use of reproductive technologies that considered their costs as well as future co-ancestry during selection

Increased genetic gains in multi-trait sheep indices using female reproductive technologies combined with optimal contribution selection and genomic breeding values.

Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile 'in vitro' fertilisation and embryo transfer (JIVET) can produce multiple offspring per mating in sheep and cattle. In breeding programs this allows for higher female selection intensity and, in the case of JIVET, a reduction in generation interval, resulting in higher rates of genetic gain. Low selection accuracy of young females entering JIVET has often dissuaded producers from using this technology. However, genomic selection (GS) could increase selection accuracy of candidates at a younger age to help increase rates of genetic gain. This increase might vary for different traits in multiple trait breeding programs depending on genetic parameters and the practicality of recording, particularly for hard to measure traits. This study used both stochastic (animals) and deterministic (GS) simulation to evaluate the effect of reproductive technologies on the genetic gain for various traits in sheep breeding programs, both with and without GS. Optimal contribution selection was used to manage inbreeding and to optimally assign reproductive technologies to individual selection candidates. Two Australian sheep industry indexes were used - a terminal sire index that focussed on growth and carcass traits (the 'Lamb 2020' index) and a Merino index that focuses on wool traits, bodyweight, and reproduction (MP+). We observed that breeding programs using artificial insemination or natural mating (AI/N) + MOET, compared with AI/N alone, yielded an extra 39% and 27% genetic gain for terminal and Merino indexes without GS, respectively. However, the addition of JIVET to AI/N + MOET without GS only yielded an extra 1% genetic gain for terminal index and no extra gain in the Merino index. When GS was used in breeding programs, we observed AI/N + MOET + JIVET outperformed AI/N + MOET by 21% and 33% for terminal and Merino indexes, respectively. The implementation of GS increased genetic gain where reproductive technologies were used by 9-34% in Lamb 2020 and 37-98% in MP+. Individual trait response to selection varied in each breeding program. The combination of GS and reproductive technologies allowed for greater genetic gain in both indexes especially for hard to measure traits, but had limited effect on the traits that already had a large amount of early age records

Increased genetic gains in sheep, beef and dairy breeding programs from using female reproductive technologies combined with optimal contribution selection and genomic breeding values

'Background': Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro embryo production and embryo transfer (JIVET) can boost rates of genetic gain but they can also increase rates of inbreeding. Inbreeding can be managed using the principles of optimal contribution selection (OCS), which maximizes genetic gain while placing a penalty on the rate of inbreeding. We evaluated the potential benefits and synergies that exist between genomic selection (GS) and reproductive technologies under OCS for sheep and cattle breeding programs. 'Methods': Various breeding program scenarios were simulated stochastically including: (1) a sheep breeding program for the selection of a single trait that could be measured either early or late in life; (2) a beef breeding program with an early or late trait; and (3) a dairy breeding program with a sex limited trait. OCS was applied using a range of penalties (severe to no penalty) on co-ancestry of selection candidates, with the possibility of using multiple ovulation and embryo transfer (MOET) and/or juvenile in vitro embryo production and embryo transfer (JIVET) for females. Each breeding program was simulated with and without genomic selection. 'Results': All breeding programs could be penalized to result in an inbreeding rate of 1 % increase per generation. The addition of MOET to artificial insemination or natural breeding (AI/N), without the use of GS yielded an extra 25 to 60 % genetic gain. The further addition of JIVET did not yield an extra genetic gain. When GS was used, MOET and MOET + JIVET programs increased rates of genetic gain by 38 to 76 % and 51 to 81 % compared to AI/N, respectively. 'Conclusions': Large increases in genetic gain were found across species when female reproductive technologies combined with genomic selection were applied and inbreeding was managed, especially for breeding programs that focus on the selection of traits measured late in life or that are sex-limited. Optimal contribution selection was an effective tool to optimally allocate different combinations of reproductive technologies. Applying a range of penalties to co-ancestry of selection candidates allows a comprehensive exploration of the inbreeding vs. genetic gain space

Accounting for the Cost of Reproductive Technologies During Selection in Sheep Breeding Programs

Female reproductive technologies, such as MOET and JIVET, have been shown to increase the rate of genetic gain. However, they incur substantial costs to breeders using them. In this work, optimal contribution selection was used to find the balance between genetic merit, co-ancestry and cost of reproductive technologies in sheep breeding programs. To offset the cost of using the reproductive technologies, breeders received a premium based on the value of the genetic gain achieved by the ram buyers. Australian terminal sire and Merino breeding programs were simulated, using industry indexes. For the terminal sire breeding program, the premium needed to be greater than 50% beforen reproductive technologies were used. In the Merino breeding program, where the standard deviation of the index is 3 times higher than the terminal index, reproductive technologies were used with lower premiums (6% and 32% premiums, respectively). For both breeding programs, the rate of genetic gain increased with more allocations of reproductive technologies. There was also a higher proportion of JIVET assigned compared to MOET, due to a lower cost per lamb. The benefits of genomic selection were greatest in the merino program, due to the higher use of JIVET. Assigning costs of reproductive technologies allows for robust and practical breeding programs to be designed