Andrew Davie

Bio: Andrew Davie is an academic researcher from University of Stirling. The author has contributed to research in topics: Labrus bergylta & Wrasse. The author has an hindex of 25, co-authored 70 publications receiving 2214 citations. Previous affiliations of Andrew Davie include NHS Lothian.

Harnessing genomics to fast-track genetic improvement in aquaculture.

Abstract: Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.

Current knowledge on the photoneuroendocrine regulation of reproduction in temperate fish species

Abstract: Seasonality is an important adaptive trait in temperate fish species as it entrains or regulates most physiological events such as reproductive cycle, growth profile, locomotor activity and key life-stage transitions. Photoperiod is undoubtedly one of the most predictable environmental signals that can be used by most living organisms including fishes in temperate areas. This said, however, understanding of how such a simple signal can dictate the time of gonadal recruitment and spawning, for example, is a complex task. Over the past few decades, many scientists attempted to unravel the roots of photoperiodic signalling in teleosts by investigating the role of melatonin in reproduction, but without great success. In fact, the hormone melatonin is recognized as the biological time-keeping hormone in fishes mainly due to the fact that it reflects the seasonal variation in daylength across the whole animal kingdom rather than the existence of direct evidences of its role in the entrainment of reproduction in fishes. Recently, however, some new studies clearly suggested that melatonin interacts with the reproductive cascade at a number of key steps such as through the dopaminergic system in the brain or the synchronization of the final oocyte maturation in the gonad. Interestingly, in the past few years, additional pathways have become apparent in the search for a fish photoneuroendocrine system including the clock-gene network and kisspeptin signalling and although research on these topics are still in their infancy, it is moving at great pace. This review thus aims to bring together the current knowledge on the photic control of reproduction mainly focusing on seasonal temperate fish species and shape the current working hypotheses supported by recent findings obtained in teleosts or based on knowledge gathered in mammalian and avian species. Four of the main potential regulatory systems (light perception, melatonin, clock genes and kisspeptin) in fish reproduction are reviewed.

Gamete quality and broodstock management in temperate fish

Abstract: The ability to fully control sexual maturation and spawning and to produce large numbers of high quality seeds ‘on demand’ (i.e. all year long) is a primary requirement for the successful development of aquaculture. This relies on optimal broodstock management practices based on extensive knowledge of the nutritional and environmental requirements of fish in captivity. However, for many established, emerging and new farmed fish species, such knowledge is limited or not available yet. The level of domestication also plays an essential role as stocks with improved traits in farming conditions are selected. Importantly, reliable indicators of egg quality are still lacking and hatcheries still rely on wild harvested broodstocks in many farmed fish species. These key challenges must be addressed urgently to ensure the sustainable development of the European fish farming sector. This review gives an overview of methods to assess egg/sperm quality and many of the most important factors affecting gamete production and quality, including broodstock nutrition, environmental and spawning induction protocols, genetic management, gamete preservation and new reproductive strategies.

Effects of climate change on fish reproduction and early life history stages

Abstract: Seasonal change in temperature has a profound effect on reproduction in fish. Increasing temperatures cue reproductive development in spring-spawning species, and falling temperatures stimulate reproduction in autumn-spawners. Elevated temperatures truncate spring spawning, and delay autumn spawning. Temperature increases will affect reproduction, but the nature of these effects will depend on the period and amplitude of the increase and range from phase-shifting of spawning to complete inhibition of reproduction. This latter effect will be most marked in species that are constrained in their capacity to shift geographic range. Studies from a range of taxa, habitats and temperature ranges all show inhibitory effects of elevated temperature albeit about different environmental set points. The effects are generated through the endocrine system, particularly through the inhibition of ovarian oestrogen production. Larval fishes are usually more sensitive than adults to environmental fluctuations, and might be especially vulnerable to climate change. In addition to direct effects on embryonic duration and egg survival, temperature also influences size at hatching, developmental rate, pelagic larval duration and survival. A companion effect of marine climate change is ocean acidification, which may pose a significant threat through its capacity to alter larval behaviour and impair sensory capabilities. This in turn impacts on population replenishment and connectivity patterns of marine fishes.

ipyrad: Interactive assembly and analysis of RADseq datasets.

Abstract: SUMMARY ipyrad is a free and open source tool for assembling and analyzing restriction site-associated DNA sequence datasets using de novo and/or reference-based approaches. It is designed to be massively scalable to hundreds of taxa and thousands of samples, and can be efficiently parallelized on high performance computing clusters. It is available both as a command line interface and as a Python package with an application programming interface, the latter of which can be used interactively to write complex, reproducible scripts and implement a suite of downstream analysis tools. AVAILABILITY AND IMPLEMENTATION ipyrad is a free and open source program written in Python. Source code is available from the GitHub repository (https://github.com/dereneaton/ipyrad/), and Linux and MacOS installs are distributed through the conda package manager. Complete documentation, including numerous tutorials, and Jupyter notebooks demonstrating example assemblies and applications of downstream analysis tools are available online: https://ipyrad.readthedocs.io/.