Annual Report: 2008

I submit herewith the annual report from the Agricultural and Forestry Experiment Station, School of Natural Resources and Agricultural Sciences, University of Alaska Fairbanks, for the period ending December 31, 2008. This is done in accordance with an act of Congress, approved March 2, 1887, entitled, “An act to establish agricultural experiment stations, in connection with the agricultural college established in the several states under the provisions of an act approved July 2, 1862, and under the acts supplementary thereto,” and also of the act of the Alaska Territorial Legislature, approved March 12, 1935, accepting the provisions of the act of Congress. The research reports are organized according to our strategic plan, which focuses on high-latitude soils, high-latitude agriculture, natural resources use and allocation, ecosystems management, and geographic information. These areas cross department and unit lines, linking them and unifying the research. We have also included in our financial statement information on the special grants we receive. These special grants allow us to provide research and outreach that is targeted toward economic development in Alaska. Research conducted by our graduate and undergraduate students plays an important role in these grants and the impact they make on Alaska.Financial statement -- Grants -- Students -- Research reports: Partners, Facilities, and Programs; Geographic Information; High-Latitude Agriculture; High-Latitude Soils, Management of Ecosystems; Natural Resources Use and Allocation; Index to Reports -- Publications -- Facult

Nutritional and environmental effects on triploid Atlantic salmon skeletal deformity, growth and smoltification

The Atlantic salmon (Salmo salar) is an iconic species that dominates the global finfish production sector with increasing market demand. The Scottish industry and government alone aspires for expansion of the sector to 210,000 t by 2020 with 154, 000 t produced in 2013. As such, there are pressures to improve sustainable development in particular to minimise the genetic impact of escapees on wild populations and reduce sea lice infection which are required for the granting of “green licenses” in Norway. The use of triploidy has been tested in the 1980’s with little success owing to suboptimal rearing conditions leading to elevated mortalities, poorer growth and a higher prevalence of deformities, in particular of the skeleton. Collectively: recent success of triploid trout farming, expansion to the salmon production sector and potential resulting pressure on wild stocks through escapee increases have reinstated interest to implement artificially induced triploid Atlantic salmon in commercial production. As diploid Atlantic salmon have undertaken extensive domestication to achieve the high quality production and welfare standards observed to date, triploid conspecifics too require husbandry optimisation to realise potential. In particular, industrialisation requires that higher observations of deformities and inconsistent growth trajectories during seawater ongrowing be resolved through optimisation of rearing regimes and subsequent standardization of husbandry protocols. Triploids possess additional genomic material and increased cell size yet reduced frequency that reflects known differences in physiology and supports that, in effect, triploids should be considered as a new species relative to diploid conspecifics. Therefore, this doctoral thesis aimed to study nutrition and temperature effects on triploid Atlantic salmon traits throughout the production cycle from ‘egg to plate’. Nutrition trials aimed to improve growth potential and mitigate skeletal deformities both in freshwater (FW) and saltwater (SW) whilst attempts were made to define a window of smoltification to ensure optimal ongrowing performance. Finally, impacts of embryonic temperature regimes that are known to impact long term performance and deformity development in triploids, were examined in relation to DNA regulation and yolk composition in an attempt to underpin potential mechanisms for the environmental impact of temperature on developmental phenotype. One of the main restrictions to triploid Atlantic salmon implementation is the increased prevalence and severity of skeletal deformities, particularly after the maring phase. The work performed in this thesis first demonstrated that protein and / or phosphorous (P) supplementation throughout SW ongrowing not only reduced the level of severely deformed (≥ 10 deformed vertebrae observable by x-radiography) individuals by 30 % but also sustained 6.8 % faster growth and improved harvest grade compared to triploids fed a standard grower diet (chapter 2). Comparison of x-radiography and severely deformed individuals between harvest and sea transfer highlighted that protein and P supplementation arrested deformity development whereas prevalence increased in triploids fed a standard grower diet. This implied that severe deformities were of FW origin and strongly suggest requirement for improved nutrition in FW to optimise SW performance. Therefore investigation of higher dietary P inclusion in FW was investigated and results showed significantly reduced number of deformed vertebrae and no severely deformed individuals in those fed 19.7 g total P Kg-1 compared with those fed 13.0 & 16.7 g total P Kg-1 (chapter 3). Most deformities were localised in the central (vertebrae 27 – 31) and caudal (vertebrae 52 – 57) regions for all treatments. However, triploids fed lower dietary P displayed a particular increase in prevalence within the tail region (vertebrae 32- 47) which is consistent with SW ongrowing reports and results from chapter 2, further highlighting FW origin of higher vertebral deformities reported in SW ongrowing in triploids. Higher P supplementation in FW also significantly improved growth in triploid parr compared to diploids and lower supplementation. However, this effect did not transpire in later FW smolt stages where weights were significantly higher in triploids fed lower compared to higher P supplementation. Expression of target genes involved in osteogenesis and bone P homeostasis in vertebrates were then analysed and a ploidy effect of osteogenic genes alp, igf1r and opn as well as a dietary effect on P homeostasis gene fgf23 was apparent in the parr stages but not smolt. In addition, stronger ploidy-diet effects were also observed in parr stages for whole body mineral concentrations. Collectively, growth, gene expression and whole body mineral content results indicate these earlier parr life stages may be more sensitive to P supplementation. This pronounced effect may be a consequence of seasonal accelerated growth associated with this period, where higher temperatures were also observed. The potential for shorter P supplementation windows in commercial production was addressed in chapter 4 with hope to cut economic cost to raw mineral inclusion in feed and also mitigate potential anthropogenic eutrophication on the environment that may be induced by P leached through uneaten feed and faeces. Triploids were fed higher dietary P (17.4 g total P Kg-1) until either early (5 g) or later (20 g) parr stages, or smolt (83 g) and monitored for performance throughout freshwater (FW) development. During later parr development (30 g), x-radiography assessment demonstrated that increased dietary P reduced the number of deformities and severely deformed individuals with no indication that feeding P for shorter windows improved skeletal integrity. Hence, P supplementation may be required throughout FW development for optimal skeletal performance. In addition, no differences in deformities were observed between triploid treatments at smolt. An effect of dietary P supplementation on whole body mineral concentration was observed in the early and later parr stages that was not as pronounced as smolt, which is consistent with results in chapter 3. Together, these results indicate that skeletal assessment during early developmental stages may not reflect smolt performance most likely as a consequence of seasonal effects of improved linear growth in the cooler winter temperatures prior to smolt where reversible deformities observed at parr may also be alleviated. In the same study (chapter 4), the inclusion of the probiotic Pediococcus acidilactici (Bactocell™) was also tested as a means to enhance gut assimilation as suggested in previous studies and therefore reduce the levels of P supplementation. Results clearly indicate superior skeletal performance in parr (30 g) as well as significantly less deformed vertebrae and no severely deformed individuals. However, at smolt (~83g), no effects of the dietary probiotic treatment were observed which may also be attributed to seasonal effects. Overall, nutritional research clearly indicate triploids require higher dietary P for optimal growth and skeletal development, which although is not consistent between life stages, is ultimately required throughout FW for optimal skeletal development at smolt. The use of probiotics offer a promising avenue for reduced P requirement in FW feed and further research should verify results and assess long-term performance. Timing of SW transfer according to correct parr-smolt transformation (PST) is essential for survival and growth performance in ongrowing where feeding and growth rate accelerate post-transfer. So far, SW transfer regimes and in particular the smoltification ‘window’ remains loosely defined in triploid Atlantic salmon and it is crucial that this be addressed to ensure optimal ongrowing survival and performance. Results in chapter 5 show that triploid Atlantic salmon reared under an ambient photo-thermal regime (S1+) have a wider smoltification window within 155 – 365 degree days as well as an earlier onset by 48 degree days. This was confirmed through raised Na+, K+ - ATPase (NKA) activity that was maintained for a longer duration and earlier skin silvering compared to diploid siblings. In addition, reduced plasma chloride (Cl-) levels alongside improved survival following SW challenge compared with diploid siblings strongly suggest that triploids had improved hypo-osmoregulatory capacity and a wider smolt window. Although other studies have demonstrated that triploid salmonids may have earlier onset of PST none to date have investigated the window duration. Results in this study need to be verified against other photo-thermal regimes; a wider smolt window may be of great benefit to industry as there is potential for reduced FW rearing periods, earlier onset of ongrowing and increased sea-transfer flexibility compared to diploid conspecifics. Suboptimal egg incubation conditions, in particular higher temperatures, are one of the primary causes of deformity in triploid Atlantic salmon. This may be associated with embryogenesis being stenothermal and also where the critical process of somitogenesis and the underlying changes in DNA regulation occur. Hence, diploid and triploid embryos were reared at temperature regimes known to be optimal and suboptimal for development (5.9, 7.9 and 10.7 ºC) from fertilisation until the eyeing stages and then at 7.8 ºC until hatch. Temperature / ploidy associated mechanisms that may induce phenotypic variation were analysed comprising of global DNA methylation (DNAme), as an indicator of DNA regulation, as well as changes in Nitrogenous metabolites (NM) including Free Amino Acid (FAA) concentrations. Differences in genomic weight between diploids and triploids may potentially impact DNA regulation and the availability of maternally provided resources such as NMs for the dramatic process of reorganisation of the methylome during embryogenesis. Although changes in NM utilisation were apparent between life stages and influenced by temperature, no impact of ploidy was evident. In addition, no impact of temperature was observed on DNAme levels. This indicates availability of maternally provided NMs and DNA programming may not necessarily be a factor in temperature induced deformities in triploids and phenotype assessment in later life-stages would verify this conclusion. In addition sequence specific DNAme results and analysis of other epigenetics process such as hitstone modification would verify or reveal other epigenetic effects. However, results did reveal interesting ploidy differences in DNAme levels post gastrulation where triploids maintained lower DNAme levels relative to diploids throughout somitogenesis indicating a delay in the DNA remethylation or reprogramming process. This is the first study to identify potential triploid specific differences in DNA reprogramming in salmonids and so verification as well as an understanding of the impact on epigenetics and long-term phenotype must be assessed. This doctoral work adds significantly to existing knowledge on improved husbandry practice of triploid Atlantic salmon through: improved nutritional regimes and understanding of PST that have potential for improved production traits including growth, reduction of skeletal deformities and reduced rearing periods. This work also pioneers study of DNA regulation in triploid embryogenesis that pose important future questions to explain fundamental differences associated with altered cellular and genomic make-up in triploids. This research will assist in enabling triploid salmon as a tool for sustainability in global aquaculture production of Atlantic salmon as demonstrated by the development of patented triploid feed in relation to these trials and optimised protocols for SW transfer. Ultimately, this additional knowledge highlights the potential for triploids to perform equally well if not better than diploid conspecific

Wildlife Decomposition in West Central Montana: A Preliminary Study Conducted to Provide Field Investigation Material and Training for Wildlife Officers

An issue with many poaching investigations is the discovery of carcasses in advanced stages of decomposition with little information to indicate time of death (TOD). To address TOD issues of carcasses found in a state of decomposition, and to provide training materials and field tools for investigating officers, this project was initiated to identify decomposition stages and to monitor decomposition rates for those stages in the west central area of Montana. A total of 15 carcasses were placed in electrified exclosures during various times of the year which provided seasonal variation and include: a pair of gray wolves (8 total) placed on the same day for each of the four seasons; a black bear placed early fall, and another middle fall; three mountain lion kittens and a whitetail deer placed late fall; and an adult mountain lion placed during the winter. Data collection included weather, photography, decomposition characteristics, and insects. It is also important to note that TOD estimates are appropriate for livestock depredation claims. It may be vital to establish the TOD of the predating carnivore to assure it was legally killed by the livestock manager when livestock were in the area

Remaking the Mazeway: Skeletal and archaeological evidence for a variant Ancestral Pueblo mortuary rite at Wallace Ruin (USA)

This thesis presents the results of a multi-disciplinary investigation of a variant Ancestral Pueblo mortuary rite at Wallace Ruin, southwest Colorado (USA). This multi-storey building is one of four Lakeview Group great houses connected to the Pueblo II regional system centred at Pueblo Bonito of Chaco Canyon some 100 km to the south. From c. AD 1060-1150, Wallace Ruin functioned as a ritual- economic centre with a small residential component. Then, habitation of this great house, the Lakeview Group and all domiciles within 10 kilometres ceased. However, three or more decades later at least six rooms were used as a non- residential, Pueblo III mortuary facility for a minimum of 32 individuals. This use was in marked contrast to the enduring Ancestral Pueblo practice of residential burial, usually in the extramural midden. The interrogation of several hypotheses concerning this anomaly entails a bioarchaeological approach that integrates skeletal evidence with spatial analyses regarding diachronic mortuary location choices at Wallace Ruin. Taphonomic methods that segregate bone displacements during corpse decomposition in a filled versus a void space provide accurate determinations of the depositional versus discovered mortuary microenvironments. The diachronic analysis of data from over 100 San Juan Region sites reveals additional ways in which Wallace’s Pueblo III mortuary program departs from longstanding communities of practice, whether great house or domicile. Chief among these are the use of a surface room floor and the postural arrangement of supine bodies with flexed knees upright. These results, in combination with material culture evidence, form the basis of this thesis: The Pueblo III mortuary program at Wallace Ruin is a variant rite that entails a Mesa Verde Region reformulation of a Pueblo Bonito house society. The sanctioned retrieval of objects of memory offers a plausible explanation for intentional intrusions into two mortuary contexts. Beyond addressing questions concerning Wallace Ruin, a major contribution of this study includes advancement of the house society model as an interpretive scheme for evaluating Mesa Verde Region socio-ritual dynamics. This research also demonstrates the effectiveness of anthropologie de terrain (Duday, 2006) to retrospectively determine the original status of Ancestral Pueblo mortuary microenvironments. The refinement developed for this study, in which Range of Motion criteria are used to detect large-scale movements of lower limbs during corpse decomposition, is suitable for bioarchaeological analyses the world over

Fish farm ecology : a conceptual framework and empirical investigation of the CSR performance of Marine Harvest ASA and Cermaq ASA

The purpose of this master thesis is to give business participants, regulatory authorities, researchers and the broader community awareness of priority areas within the fish farming industry. In this sense, we have developed a conceptual framework; Fish Farm Ecology (FFE). The FFE model equates three spheres; economy, ecology, and ichthyology. It has flexibility and can be used both as an analytical tool for a broader interest group and as a management tool for companies within the industry. The conceptual framework and the empirical investigation are based upon five context areas; fish feed, sea cages, escaping, sea lice, and the slaughter process. In the empirical investigation, which is concentrated around two companies; Marine Harvest ASA and Cermaq ASA, perspectives of CSR and ethics are included. The CSR-FFE performance of Marine Harvest lies within the upper edge of a minor link, while Cermaq’s lies within the intermediate link

New fish product ideas generated by European consumers

Food lifestyles are changing; people have less time to spend on food purchase and preparation, therefore leading to increasing demand for new food products. However, around 76% of new food products launched in the market fail within the first year (Nielsen, 2014). One of the most effective ways to enhance new products’ success in the market is by incorporating consumers’ opinions and needs during the New Product Development (NPD) process (Moon et al., 2018). This study aimed to explore the usefulness of a qualitative technique, focus groups, to generate new aquaculture fish product ideas as well as to identify the most relevant product dimensions affecting consumers’ potential acceptance.Peer ReviewedPostprint (published version

PRODUCTION, EXCHANGE AND SOCIAL INTERACTION IN THE GREEN RIVER REGION OF WESTERN KENTUCKY: A MULTISCALAR APPROACH TO THE ANALYSIS OF TWO SHELL MIDDEN SITES

The Green River region of western Kentucky has been a focus of Archaic period research since 1915. Currently, the region is playing an important role in discussions of Archaic hunter-gatherer cultural complexity. Unfortunately, many of the larger Green River sites contain several archaeological components ranging from the Early to Late Archaic periods. Understanding culture change requires that these multiple components somehow be sorted and addressed individually. Detailed re-analyses of Works Progress Administration (WPA) era artifact collections from two archaeological sites in the Green River region – the Baker (15Mu12) and Chiggerville (15Oh1) shell middens – indicate that these sites are relatively isolated Middle and Late Archaic components, respectively. The relatively unmixed character of Baker and Chiggerville makes these sites excellent candidates for evaluating aspects of complexity during the Archaic. After developing a theoretical basis for evaluating the relative complexity of the social organization of the Baker and Chiggerville site inhabitants on the basis of the material record they left behind, I employ detailed analyses of the bone, antler, and stone tools from these two sites to examine six microscalar aspects of complexity – technological organization, subsistence, specialization, leadership, communication networks, and exchange. These microscalar aspects of complexity all can be linked materially to the archaeological record of the Green River region and can be evaluated as proxies for changes in social organization among the hunter-gatherers who inhabited this region during the Middle and Late Archaic periods. Although the Baker assemblage indicated greater complexity in communication networks and certain proxies for leadership and technological organization, most indicators suggest that the Chiggerville site inhabitants were the more complexly organized group and were in the process of developing a tribal-like social formation. This research, therefore, tentatively supports the hypothesis of increasing complexity through time during the Archaic. However, marked differences in the technological strategies utilized by the Baker and Chiggerville site inhabitants indicates these groups may not have been historically related, thereby violating one of the primary assumptions of the project. If this alternative hypothesis is confirmed through additional research, then no conclusions concerning change through time can be derived from this study