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Journal ArticlePublication Accuracy of genotype imputation in sheep breeds(Wiley-Blackwell Publishing Ltd, 2012) ;Hayes, B J ;Bowman, P J ;Daetwyler, H D ;Kijas, J WAlthough genomic selection offers the prospect of improving the rate of genetic gain in meat, wool and dairy sheep breeding programs, the key constraint is likely to be the cost of genotyping. Potentially, this constraint can be overcome by genotyping selection candidates for a low density (low cost) panel of SNPs with sparse genotype coverage, imputing a much higher density of SNP genotypes using a densely genotyped reference population. These imputed genotypes would then be used with a prediction equation to produce genomic estimated breeding values. In the future, it may also be desirable to impute very dense marker genotypes or even whole genome re-sequence data from moderate density SNP panels. Such a strategy could lead to an accurate prediction of genomic estimated breeding values across breeds, for example. We used genotypes from 48 640 (50K) SNPs genotyped in four sheep breeds to investigate both the accuracy of imputation of the 50K SNPs from low density SNP panels, as well as prospects for imputing very dense or whole genome re-sequence data from the 50K SNPs (by leaving out a small number of the 50K SNPs at random). Accuracy of imputation was low if the sparse panel had less than 5000 (5K) markers. Across breeds, it was clear that the accuracy of imputing from sparse marker panels to 50K was higher if the genetic diversity within a breed was lower, such that relationships among animals in that breed were higher. The accuracy of imputation from sparse genotypes to 50K genotypes was higher when the imputation was performed within breed rather than when pooling all the data, despite the fact that the pooled reference set was much larger. For Border Leicesters, Poll Dorsets and White Suffolks, 5K sparse genotypes were sufficient to impute 50K with 80% accuracy. For Merinos, the accuracy of imputing 50K from 5K was lower at 71%, despite a large number of animals with full genotypes (2215) being used as a reference. For all breeds, the relationship of individuals to the reference explained up to 64% of the variation in accuracy of imputation, demonstrating that accuracy of imputation can be increased if sires and other ancestors of the individuals to be imputed are included in the reference population. The accuracy of imputation could also be increased if pedigree information was available and was used in tracking inheritance of large chromosome segments within families. In our study, we only considered methods of imputation based on population-wide linkage disequilibrium (largely because the pedigree for some of the populations was incomplete). Finally, in the scenarios designed to mimic imputation of high density or whole genome re-sequence data from the 50K panel, the accuracy of imputation was much higher (86-96%). This is promising, suggesting that in silico genome re-sequencing is possible in sheep if a suitable pool of key ancestors is sequenced for each breed.1104 1 - Some of the metrics are blocked by yourconsent settings
Journal ArticlePublication Acute stress enhances sensitivity to a highly attractive food reward without affecting judgement bias in laying hens(Elsevier BV, 2015) ;Hernandez, Carlos E; ;Lea, Jim; Affective states can be evaluated by assessing shifts in the animal's expectation of a positive and negative outcome in response to ambiguous cues, also known as judgement bias (JB). The aim of this study was to use a JB methodology, using a go/go type of task where animals are required to make an active choice, to assess the effects of acute stress on affective states in hens. Thirty ISA-Brown hens were trained in a two-choice (left-right) test in an arena to associate a high-value (H) reward (four mealworms) with a 100% black and a low-value (L) reward (one mealworm) with 5% black (visually white) cues. Twenty hens that learnt the tasks were randomly allocated to either a control (C) or stress (S; 5 min social isolation in a novel environment) group. During testing, hens were presented with H and L (rewarded) and three novel ambiguous (un-rewarded) cues: 75%, 50% and 25% black. Order of cue presentation was balanced between treatments to either having ambiguous cues always preceded by L cues (L-Ambiguous) or by H cues (H-Ambiguous). Latency to approach a reward and active choice made (i.e. reaching side associated with either H or L reward) were recorded.1522 - Some of the metrics are blocked by yourconsent settings
Journal ArticlePublication Agricultural Land Abandonment in the Hill Agro-ecological Region of Nepal: Analysis of Extent, Drivers and Impact of Change(Springer New York LLC, 2021-06) ;Subedi, Yuba Raj; ; Ojha, Roshan BabuDespite widely reported trends of agricultural land abandonment across many parts of the globe, this land use change phenomenon is relatively new in the context of Nepal. In recent years, rural farming communities in the hill region are gradually reducing the intensity of farming, leading to underutilisation and abandonment of agricultural lands. Adopting a mixed methods research approach, this study investigated the extent of agricultural land abandonment, its underlying causal drivers and perceived impacts in the hill agro-ecological region of Nepal. A structured survey of 374 households and six focus group discussions were carried out in three districts. The study revealed that around 40% of agricultural lands in the hill agro-ecological region have been abandoned and 60% of farmers have left at least one parcel of agricultural land abandoned. It was found that biophysical drivers (distance from homestead to parcel, slope of the parcel, land fragmentation, land quality and irrigation availability) and socio-demographic drivers (family size, higher education of the household members, domestic migration and out-migration) were responsible for agricultural land abandonment. Negative impacts of land abandonment were observed on the rural landscape, human-made farm structures, socio-economic systems, local food production and food security. In line with global studies, this research suggest that marginal land quality, demographic changes and rising alternative economic opportunities elsewhere contribute to farmland abandonment. This study also discusses land management approaches and policy implications to address the issue of agricultural land abandonment.1548 7 - Some of the metrics are blocked by yourconsent settings
Journal ArticlePublication Application of Testis Germ Cell Transplantation in Breeding Systems of Food Producing Species: A ReviewA major benefit of advanced reproduction technologies (ART) in animal breeding is the ability to produce more progeny per individual parent. This is particularly useful with animals of high genetic merit. Testis germ cell transplantation (TGCT) is emerging as a novel reproductive technology with application in animal breeding systems, including the potential for use as an alternative to artificial insemination (AI), an alternative to transgenesis, part of an approach to reducing generation intervals, or an approach toward development of interspecies hybrids. There is one major difference in TGCT between rodents and some other species associated with immunotolerance in heterologous transplantation. In particular, livestock and aquatic species do not require an immunesuppression procedure to allow donor cell survival in recipient testis. Testicular stem cells from a genetically elite individual transplanted into others can develop and produce a surrogate male - an animal that produces the functional sperm of the original individual. Spermatozoa produced from testis stem cells are the only cells in the body of males that can transmit genetic information to the offspring. The isolation and genetic manipulation of testis stem cells prior to transplantation has been shown to create transgenic animals. However, the current success rate of the transplantation procedure in livestock and aquatic species is low, with a corresponding small proportion of donor spermatozoa in the recipient's semen. The propagation of donor cells in culture and preparation of recipient animals are the two main factors that limit the commercial application of this technique. The current paper reviews and compares recent progress and examines the difficulties of TGCT in both livestock and aquatic species, thereby providing new insights into the application of TGCT in food producing animals.1248 1 - Some of the metrics are blocked by yourconsent settings
Conference PublicationPublication Autonomous counting of livestock from remote sensing imagery(AgResearch Grasslands, 2012); ; ; ; One of the key issues facing pastoralists across Northern Australia is accurately estimating the number of cattle they have on their property. For smaller producers this has implications in terms of optimising stocking rates to match available resources, thus ensuring sustainability and economic viability. In addition to this, for larger operations, the lack of knowledge about the number of stock has implications for account reporting and ultimately impacts on a number of financial factors including interest rate pricing, costing these operations substantial amounts of money. From a national perspective, the impending emissions trading scheme provides an opportunity for producers to gain benefits from better livestock management, however a lack of information on livestock numbers will certainly limit this. Existing techniques for counting livestock require extensive infrastructure (e.g. camera systems at water points) or devices to be applied to the animal (e.g. RFID tags), all of which are largely impractical solutions for rangeland deployment. In this preliminary study we explored the potential for remotely sensed imagery and image analysis techniques to deliver estimates of livestock populations in a pastoral environment. Airborne imagery was collected using a multispectral system with a spatial resolution of 15cm. A false colour image was developed and used in the subsequent analysis.1608 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessResearch Report For An External Body - Industry ReportB.FLT.0244: Graded levels of woodchip during wet feedlot conditions(Meat and Livestock Australia Limited, 2019-05-30); ;Tait, Amy; ; ; This project was conceived to determine the production and management costs and benefits of providing woodchip bedding to feedlot cattle during wet feedlot conditions. A randomised block design using three treatments, each with ten replicate pens of ten cattle, was conducted over a 109 day experimental period during winter (May - September 2018). The project simulated wet winter conditions using an irrigation system that provided 74 mm of rainfall per 30 day period, applied over 16 rainfall days per period and which wetted the entire pen surface, all cattle and the feedbunk of each pen. The three experimental treatments were 1) no bedding (Control), 2) bedding provided at 54 kg/m², equivalent to a bedding cost of 30 c/head.day (W30) and 3) bedding provided at 108 kg/m², equivalent to a bedding cost of 60 c/head.day (W60).
Provision of woodchip bedding at 54 kg/m² (W30) increased average daily gain (2.43 kg/hd.d, cf. 2.27 kg/hd.d for control, P = 0.003) and HSCW, yielding an additional 9.3 kg of HSCW (P = 0.001) compared to the control. There was no additional production benefit of providing double the amount of woodchip (W60). Provision of woodchip bedding had no effect on dry matter intake. As a result, conversion of gain from feed improved for W30 (0.205) and further for W60 (0.217) compared to control (0.197) (P = 0.012). There was no relationship between treatment and any other carcase attributes apart from HSCW and raw eye muscle area. It was concluded that there was no overall effect of treatment on behavioural signs of cattle welfare. However, there was a numerical effect of treatment on relative adrenal weight, such that W60 cattle were lower than W30, which were in turn lower than control cattle, indicating reduced chronic stress in woodchip bedded cattle. Woodchip bedding improved the pad score, but after week 10, the score of the pad in W30 also began to worsen, indicating that for medium and long-fed cattle, additional woodchip application may be required.
There was a $74 increase in carcase value from applying woodchip bedding at W30 and W60 rates. Using the input costs of the experiment, there was a numerical net economic benefit from the W30 treatment over the unbedded cattle, but this was highly variable and sensitive to input costs. Future research is needed at commercial scale to fully understand the economic benefits of woodchip bedding in a range of production systems.2245 6 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessResearch Report For An External Body - Industry ReportB.FLT.1005: Survey of Australian feedlot drinking water quality(Meat and Livestock Australia Limited, 2019-07-07); ; ; Jewell, MargaretHigh concentrations of Total Dissolved Solids (TDS) and salts in drinking water, often exacerbated by drought conditions, have been reported to have a detrimental impact on cattle health and performance. This research investigated water quality parameters including TDS and salts (sodium, calcium, magnesium, potassium, aluminium, zinc, iron, manganese, carbonate, bicarbonate, sulphate, nitrate and nitrite). The project summarised the range of TDS and salts in feedlot drinking water across Australia, thus determining potential impacts on cattle health and production. Additionally, feedlots using surface water sources for drinking water had the cyanobacteria species present identified and quantified. Such a study has not previously occurred in Australia.
The study was split into four parts with this report including over 100 historical water samples taken prior to 2018; 68 feedlot managers/owners completed the survey regarding water use delivered in paper and online format; 82 water samples from April to June 2019 from 58 feedlots were analysed for a suite of parameters. Where multiple water sources were used, the source water was analysed, this occurred for 24 samples. Additionally, water samples that included surface water were analysed for cyanobacteria (27 samples). Feedlots participating in the project were equivalent to over 50% of the licenced cattle feedlots.
Of the 68 feedlots completing the paper based and online survey, the majority (64%) source their cattle drinking water from groundwater. On a per-head basis, the use of groundwater as a drinking water source became even more important, covering two thirds of surveyed feedlot cattle. Surface water from dams and rivers were also a common source of water, and less common sources included reverse osmosis treated water from coal seam gas operations, tank roof water, and irrigation water.
The majority of feedlots (75%) were not aware of any issues with their drinking water quality. Of those that indicated that they had concerns about their water quality, seven feedlots identified cyanobacteria (Blue green algae) and Escherichia coli as an issue; four identified turbidity and scale (likely from calcium build up) clogging floats; and four feedlots reported that they now treat water for use in their boiler, but do not treat for cattle, while one feedlot identified high iron as an issue for boiler water.
Among trough water samples analysed for TDS, the majority (86 %) were considered satisfactory for cattle consumption and would not be expected to limit animal performance (≤ 3,000 mg/L). There were, however, cases of poor water quality identified. The highest TDS reported was 11,600 mg/L in groundwater. This water was shandied with surface water and was the maximum in the mixed trough water (5,400 mg/L), which would be expected to limit cattle performance (NASEM, 2016). Chloride was present in the highest concentration of all anions analysed. Nitrate concentrations were highest in the groundwater samples with only one trough sample exceeding the nitrate concentration threshold of 20 mg/L (NASEM, 2016). Sulphate ranged from undetected (<0.3 mg/L sulphur as sulphate) to 575 mg/L, with the highest values in groundwater samples, all samples were below the 1,000 mg/L guideline (ANZEC, 2000). Only 3% of trough samples exceeded the ANZEC (2000) limit of 5 mg aluminium/L. Manganese concentration was highest in surface water samples with 57% to 90% of trough water samples sourced from surface water exceeding the 0.05 mg/L upper-limit guideline (NASEM, 2016). The biological significance of high manganese waters remains to be elucidated, although water concentrations are well below the Maximum tolerable limit reported for dietary Manganese of 1000 mg/kg dry matter (NASEM, 2016). Two surface water samples were in excess of the trigger value for Microcystis aeruginosa (11,500 cells/mL) and were reanalysed and tested for toxins. Only one sample was below a pH 5.1 and one sample above pH of 9.
Several water treatment scenarios were investigated with distributors and installers in Australia with reverse osmosis being the most suitable treatment option. As there are no Australian references for the effect of water quality on the performance of the cattle, Patterson et al. (2004), a publication from the USA, was used for the analysis of benefit and cost of water treatment with reverse osmosis. Treatment with reverse osmosis lead to increased, and more cost-effective, cattle productivity. However, the water used in the article by Patterson et al. (2004) had high sulphate concentrations, so the same responses are unlikely with Australian water. Future research testing water quality in the range of variation experienced by Australian feedlots, in a controlled manner, would allow the industry to determine the most relevant animal production gains and thus the benefits of reverse osmosis.
In conclusion, water quality was determined to be of suitable quality for the majority of feedlots surveyed. Isolated cases of poor water quality were identified. This project is beneficial to the industry as it has yielded a comprehensive understanding of the current sources and quality of feedlot drinking water for a single point in time. Overall, this project will improve feedlot decision-making regarding the conditions when water quality parameters may impact animal health and production in beef cattle feedlots.
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Publication Open AccessDatasetBehavioural responses of Onthophagus squalidus, Onthophagus consentaneus (Scarabaeidae), Saprinus cupreus (Histeridae), and Liparochrus sp. (Hybosoridae) to experimental warming, soil moisture, and dung availability in New South Wales, AustraliaClimate change and resulting conditions like droughts and extreme heat have resulted in a loss of species diversity. Assessing how ecosystem service providers such as coprophagous beetles cope with these changes is vital to maintaining ecosystem health. The effects of increasing temperature in both moist and dry soil are explored, as is the question of whether dung’s presence (food resource) plays a role. Four beetle species – two dung beetles (Scarabaeidae: Onthophagus consentaneus and Onthophagus squalidus) and two coprophagous (Histeridae: Saprinus cupreus and Hybosoridae: Liparochrus sp.) – are examined. Six beetles of each species were placed inside a heat chamber at four different temperatures: 25 °C, 30 °C, 35 °C, and 40 °C. Each heat chamber only contained one species type, and, for each temperature, beetles were exposed to dry soil with dung, moist soil with dung, dry soil without dung, and moist soil without dung. Beetles were able to leave their chambers at any time and chambers were left active for 168 hours. Results show that Liparochrus sp. always left the chambers before 72 hours, regardless of conditions. Saprinus cupreus was unaffected by temperature and soil moisture, mostly remaining in the chambers for the full 168 hours if dung was available and leaving when not. Both dung beetle species were unaffected by temperature and soil moisture when dung was present. When dung was removed at 25 °C and 30 °C in dry soil, beetles all left the chambers, however at 35 °C and 40 °C most beetles remained in the chambers. All dung beetles left the chambers when soil was moist, and no dung was available at all four temperatures. This paper shows how dung beetle behaviour changes at high temperatures in dry soil, both when food is present and when it is not. In contrast, other coprophagous beetle species (such as S. cupreus) leave when no dung is available regardless of soil moisture and temperature.100 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessConference PublicationBESSiE: A Program for Multivariate Linear Model BLUP and Bayesian Analysis of Large Scale Genomic Data(Association for the Advancement of Animal Breeding and Genetics (AAABG), 2015); BESSiE is a software designed for uni- and multivariate analysis of linear mixed models including large scale genomic data. BESSiE facilitates models allowing for various fixed and random effects, and for observations on continuous or categorical scales, and implements different Bayesian algorithms for the prediction of effects of genetic markers (e.g. BayesA, BayesB, BayesCπ and BayesR), GBLUP and SNP-BLUP.2469 2 - Some of the metrics are blocked by yourconsent settings
Conference PublicationPublication Cattle grazing in alpine Australia. Where, When and Why?(AgResearch Grasslands, 2012) ;Ingram, Lachlan J ;Odeh, Inakwu ;Bishop, Thomas; ;Taranto, MariaAdams, Mark AGrazing of cattle in the high country of south-eastern Australia during summer and early-autumn has historically played an important role in allowing resting of pastures in lower lying regions. There are, however, remarkably few sound scientific studies undertaken to determine how cattle graze in these areas and thus where their impact may be greatest. The aim of this study was to determine the grazing patterns of a commercial beef herd grazing in the high country using GPS enabled collars. The study was undertaken a 500 ha privately owned property that borders Kosciuzko NP in southern NSW. The property varies in altitude from ca. 1450-1750 m and contains a mix of alpine grasslands and wooded (predominantly snow gums) vegetation. While not directly associated with this study, the property also encompasses the HighFire project, a long-term fully replicated fire x grazing interaction study being undertaken in these same vegetation communities.1064 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessDatasetComparative performance of scarab dung beetles to coprophagous beetles in dung removal and soil water runoff in a drought-prone habitatBeetles improving soil nutrients by burying dung is a crucial ecological process for maintaining soil health, and the tunnels created by this process improves soil infiltration and reduce soil water runoff, a vital process during droughts. This study compares the effectiveness of two native dung beetles (Scarabaeidae) with two other coprophagous beetles, a member of the Histeridae (Saprinus cupreus) and Hybosoridae (Liparochrus sp.) family. Mesocosms with a 100-gram dung pat were used in the field to produce all five treatments: a closed control mesocosm with no beetles, an open mesocosm, a closed mesocosm with coprophagous beetles, a closed mesocosm with dung beetles, and a closed mesocosm with both coprophagous and dung beetles (beetle species depended on location). After 48 hours, the dung was removed, dried, weighed, and then placed a rainfall simulator over the mesocosms to record soil water runoff. The five treatments from both locations were analysed separately. The findings show that the Saprinus cupreus and Liparochrus sp. contributed significantly to dung removal. There were significant differences in soil water runoff across the treatments, with O. consentaneus (was the best at reducing soil water runoff, with a mean reduction of 53.3%, while S. cupreus was the least effective contributing only a 28.8% mean reduction. The species O. squalidus reduced soil water runoff by 46.9%, while Liparochrus sp. reduced the mean soil water runoff by 43.9%. This investigation highlighted the need to reassess and improve our ecological management approaches including various coprophagous insect species, while understanding their collective significance in maintaining soil health.124 1 - Some of the metrics are blocked by yourconsent settings
Conference PublicationPublication Development and application of real-time sensors for enhancing productivity and efficiency at pasture(AgResearch Grasslands, 2012) ;Paull, David ;Greenwood, Paul ;Valencia, Phil ;Overs, Les; Purvis, Ian WWe are undertaking a project that will develop technologies that can be used to measure efficiency of production on pasture for cattle and sheep and then use these technologies to develop applications that lead to enhanced efficiency of production. More specifically, the project will initially prove up a benchmark system to provide accurate, precise data against which techniques and technologies that estimate intake by individual animals on pasture can be ground-truthed. The objectives are: 1. Use real-time sensors and sensor network technologies to develop predictive algorithms for individual animal intake of pasture; 2. Ground-truth these predictive algorithms using chemical markers and biomass disappearance techniques and quantify repeatability and robustness for individual animals; 3. Evaluate predictive algorithms on groups of animals grazing together against chemical markers; 4. Undertake a small-scale proof of concept study on a herd/flock basis as a lead in to genetic evaluation project.1164 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessConference PublicationThe Distribution of Risk and Reward in Extensive Livestock Improvement Systems, Their Consequences and Possible ResponsesA range of players or sectors make investments into genetic improvement in the extensive livestock industries, but overall returns are heavily dependent on decisions made by bull- (and ram-) breeders. They in turn rely on sales of genetic material to cover their own investments and maintain profitability. Some broad-scale characteristics of the investments and of the markets for genetic material are reviewed, leading to the observation of very high uncertainty in those markets. This uncertainty is almost certainly acting as a brake on genetic progress, and some possible approaches to reduce the uncertainty are considered. Such approaches will aim to improve efficiency of the market for genetic material, and will need to be designed to be robust, transparent and simple and cheap to apply.2262 1 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessJournal ArticleEffect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction(Wiley-Blackwell Verlag GmbH, 2019) ;Gowane, Gopal R; ; ; ;Al-Mamun, Hawlader AReference populations for genomic selection usually involve selected individuals, which may result in biased prediction of estimated genomic breeding values (GEBV). In a simulation study, bias and accuracy of GEBV were explored for various genetic models with individuals selectively genotyped in a typical nucleus breeding program. We compared the performance of three existing methods, that is, Best Linear Unbiased Prediction of breeding values using pedigree-based relationships (PBLUP), genomic relationships for genotyped animals only (GBLUP) and a Single-Step approach (SSGBLUP) using both. For a scenario with no-selection and random mating (RR), prediction was unbiased. However, lower accuracy and bias were observed for scenarios with selection and random mating (SR) or selection and positive assortative mating (SA). As expected, bias disappeared when all individuals were genotyped and used in GBLUP. SSGBLUP showed higher accuracy compared to GBLUP, and bias of prediction was negligible with SR. However, PBLUP and SSGBLUP still showed bias in SA due to high inbreeding. SSGBLUP and PBLUP were unbiased provided that inbreeding was accounted for in the relationship matrices. Selective genotyping based on extreme phenotypic contrasts increased the prediction accuracy, but prediction was biased when using GBLUP. SSGBLUP could correct the biasedness while gaining higher accuracy than GBLUP. In a typical animal breeding program, where it is too expensive to genotype all animals, it would be appropriate to genotype phenotypically contrasting selection candidates and use a Single-Step approach to obtain accurate and unbiased prediction of GEBV.1333 252 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessJournal ArticleEstimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihoodWe explore the estimation of uncertainty in evolutionary parameters using a recently devised approach for resampling entire additive genetic variance- covariance matrices (G). Large-sample theory shows that maximum-likelihood estimates (including restricted maximum likelihood, REML) asymptotically have a multivariate normal distribution, with covariance matrix derived from the inverse of the information matrix, and mean equal to the estimated G. This suggests that sampling estimates of G from this distribution can be used to assess the variability of estimates of G, and of functions of G. We refer to this as the REML-MVN method. This has been implemented in the mixed-model program WOMBAT. Estimates of sampling variances from REML-MVN were compared to those from the parametric bootstrap and from a Bayesian Markov chain Monte Carlo (MCMC) approach (implemented in the R package MCMCglmm). We apply each approach to evolvability statistics previously estimated for a large, 20-dimensional data set for Drosophila wings. REML-MVN and MCMC sampling variances are close to those estimated with the parametric bootstrap. Both slightly underestimate the error in the best-estimated aspects of the G matrix. REML analysis supports the previous conclusion that the G matrix for this population is full rank. REML-MVN is computationally very efficient, making it an attractive alternative to both data resampling and MCMC approaches to assessing confidence in parameters of evolutionary interest.2109 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessJournal ArticleEstimation of genomic prediction accuracy from reference populations with varying degrees of relationshipGenomic prediction is emerging in a wide range of fields including animal and plant breeding, risk prediction in human precision medicine and forensic. It is desirable to establish a theoretical framework for genomic prediction accuracy when the reference data consists of information sources with varying degrees of relationship to the target individuals. A reference set can contain both close and distant relatives as well as `unrelated' individuals from the wider population in the genomic prediction. The various sources of information were modeled as different populations with different effective population sizes (Nₑ). Both the effective number of chromosome segments (Mₑ) and Nₑ are considered to be a function of the data used for prediction. We validate our theory with analyses of simulated as well as real data, and illustrate that the variation in genomic relationships with the target is a predictor of the information content of the reference set. With a similar amount of data available for each source, we show that close relatives can have a substantially larger effect on genomic prediction accuracy than lesser related individuals. We also illustrate that when prediction relies on closer relatives, there is less improvement in prediction accuracy with an increase in training data or marker panel density. We release software that can estimate the expected prediction accuracy and power when combining different reference sources with various degrees of relationship to the target, which is useful when planning genomic prediction (before or after collecting data) in animal, plant and human genetics.1227 231 - Some of the metrics are blocked by yourconsent settings
Journal ArticlePublication Flawed mothering or infant signaling? The effects of deficient acoustic cues on ovine maternal response(John Wiley & Sons, Inc, 2018-12); ; ;Small, AlisonThe neonate distress cry, which displays a similar acoustic structure across a range of mammalian species, is highly effective in attracting, even compelling, parental care. However, if this cry is defective, as found in human and rodent neonates with poor neurobehavioral function, is the signal less enticing? Using playback recordings of a ewe's own co‐twins as stimuli in a two choice test, we compared the preference of each sheep dam for acoustic features of lamb distress calls to assess the impact of signal quality on maternal response. The results of this study indicate that lamb vocalizations with acoustic parameters reflecting poor vocal fold engagement and arousal were less likely to be preferred by their dam. Additionally, these calls were associated with delayed vocal initiation and poor infant survival behavior suggestive of subtle cognitive deficit; and support the possibility that, as in deer and rodents, ovine vocalizations within a specific fundamental frequency range may well be a trigger for optimal maternal behavior. This research has important implications for understanding failed maternal-young interactions in ungulate and other species, and for verifying standardization of infant stimuli used in maternal behavior studies.1950 3 - Some of the metrics are blocked by yourconsent settings
Thesis DoctoralPublication Fly (Diptera) Pollination Efficiency and Reproductive Needs within Crop Agroecosystems(University of New England, 2024-05-09); ; ; ; ; Spurr, CameronGlobal agricultural crop production has become increasingly pollinator-dependant. Eusocial bee taxa within the family Apidae (e.g., honey bees, bumble bees, stingless bees) are wellestablished, successful crop pollinators globally. In particular, the ubiquity and wellestablished management of the European honey bee (Apis mellifera Linnaeus, 1758) has resulted in an overreliance of this pollinator worldwide. As other non-bee insects are also effective pollinators, it has become increasingly important to better understand the capability and life history needs of non-bee pollinator taxa so they can provide alternative, or supplementary, pollination services to managed bees and be supported within the landscape. This will ensure that consistent and reliable pollination services continue to be supplied to agricultural systems. This thesis investigates the pollination effectiveness and reproductive needs of the second most important pollinator taxon behind bees, the flies (Diptera), in pollinator-dependant food crops.
First, I conducted a systematic literature review on the diets and habitat needs of 431 crop flower-visiting fly species found globally and collated the existing information into a database. I was able to document the diets and habitat needs of 242 crop-visiting fly species (24 families and 119 genera) inhabiting all eight global biogeographical regions. I found that these crop-visiting fly species live in 35 different natural habitats and belong to 10 different feeding guilds. The results of this review identified major gaps in our understanding of the life history needs of crop-pollinating flies. In particular, current floral management schemes are largely focused on the resource needs of bees. As flies require other non-floral habitats to complete their life cycles, the diverse life history needs of flies and other non-bee taxa are not currently supported by existing pollinator management practices.
Second, I investigated the identity and efficiency of floral visitors to carrot seed crops. To do this, I conducted floral field surveys and pollen deposition trials across two years (2020-21) within varying environmental conditions in the Riverina region of New South Wales (NSW). I conducted 268 floral visitation surveys and identified 53 different insects (26 families) as floral visitors of seed carrot in temperatures ranging from 10.5ºC to 39.5 ºC and in 19.7% to 94.7% relative humidity. Spatial and temporal complementarity was observed across all dominant taxonomic groups (ladybeetles, bees, flies). Wild taxa generally matched managed honey bees in terms of abundance and their capability to transfer pollen between carrot parent lines. Further, wild taxa, not managed European honey bees deployed for pollination services, are providing the bulk of pollination services to Australian hybrid seed carrot.
Third, I determined the oviposition and habitat needs of pollinating hoverflies (Syrphidae: Eristalini). I did this by deploying 14 portable pools filled with soil and decaying vegetation across four seed carrot sites in the Riverina (NSW) region of Australia. All pools successfully supported the immature stages (eggs and larvae) of hoverflies after 12 to 21 days, and two beneficial species of flies were reared from the pools: Eristalinus punctulatus and Eristalis tenax (Linnaeus, 1758). Both species were effective pollinators of seed carrot in Chapters Three and Four of this thesis, respectively. These results suggest that deploying portable habitat pools filled with decaying plant materials in agroecosystems may be a successful management intervention to rapidly facilitate hoverfly pollinator reproduction.
Fourth, I assessed the effectiveness of the Australasian endemic golden native dronefly Eristalinus punctulatus (Macquart, 1847), at transferring pollen to hybrid seed carrot flowers. While both honey bees and the native drone fly were capable of depositing pollen onto seed carrot floral stigmas, golden native drone flies on average deposited more pollen onto stigmas than European honeybees. I also observed the first recorded event of natural oviposition of this fly species on the Mid North Coast (NSW) region. When observing the oviposition of this fly, I found that they oviposited within discarded raspberry plant root balls at a commercial berry farm. This observation, coupled with their demonstrated pollination effectiveness in seed carrot, suggests that these endemic flies could be supported as potential pollinators by deploying non-floral habitat within agroecosystems.
Finally, I compared the pollination effectiveness and activity patterns of two managed fly pollinators and two managed bee species at commercial raspberry and blackberry farms in two major berry growing regions in Australia: Mid North Coast (NSW) and Northern Tasmania (TAS). All taxa were capable of effectively pollinating raspberry and blackberry after one visit to a flower; however, the quality, weight, and number of pollinated drupelets per fruit varied depending on the taxa tested. In small cages, E. tenax and wild taxa pollinated raspberry fruits that weighed significantly more and were of higher quality than fruits harvested from C. stygia cages; however, there were no significant differences in the quality, weight, and number of pollinated drupelets in blackberry across all taxa. Further, in a blackberry polytunnel in Tasmania, E. tenax flies were significantly more active than European honey bees, and the fruits harvested from the E. tenax polytunnel did not differ from fruits visited by honey bees. These results demonstrate that some fly species could be effective supplementary, or alternative, pollinators to managed bees in commercial raspberry and blackberry.
This thesis demonstrates the importance of understanding how wild taxa, like flies and non-Apis bees, contribute to pollination service delivery, and how best to support these taxa within agroecosystems. Some flies and other wild taxa can provide significant and effective pollination services to some crops. If supported with foraging and habitat needs, these taxa may be able to provide similar pollination services to the honey bees used within these systems. Identifying wild pollinator taxa and their life history needs, assessing their capability as pollinators in a variety of crop systems, developing rearing techniques to commercialize effective taxa, and methods to support effective wild and managed pollinator assemblages within agroecosystems, are all important next steps to improve pollination services and yields of pollinator-dependant cropping systems globally.
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Publication Open AccessDatasetFly (Diptera) pollination efficiency and reproductive needs within crop agroecosystems - Dataset(University of New England, 2024); ; ; ;Spurr, Cameron; ;Australian Museum ;seedPurity Pty Ltd ;Costa Exchange GroupSouth Pacific Seeds Pty LtdThis dataset consists of eight tabs (the first four relating to Chapter 2 and the remaining four relating to Chapters 3, 4, 5, and 6 of my thesis). All data related to this thesis was collected online from the Web of Science and Scopus search engines (Chapter 2), the CropPol and Rader et al. 2020 public databases, and in the field from Griffith, New South Wales, Australia (Chapters 3, 4, and 5), from the East-North Coast of New South Wales, Australia (Chapter 6), and from Northern Tasmania, Australia (Chapter 6). Each tab has an excel spreadsheet with data from each thesis research chapter, and the content of each tab is explained below: Chapter 2.1: A review of the life history needs of the larval and adult stages of crop flower-visiting flies (Diptera). This dataset consists of family, genus, and species names extracted from public pollination databases ('CropPol' or 'Rader et al. 2020'), the total number of searches the species name received from Scopus and/or WOS (Web of Science), whether the information for the diet and habitat needs were found ('Accessible' or 'Inaccessible'), the total number of larval and adult feeding guilds the fly may utilize ('Unknown', 'One', 'Two', 'Three', 'Four', 'Five', or 'Six'), whether the fly utilizes the same feeding guilds in both active developmental stages of life ('Unknown', 'Different', or 'Same'), and finally the dataset in which the species name was extracted from ('CropPol' or 'Rader et al. 2020'). Chapter 2.2: A review of the life history needs of the larval and adult stages of crop flower-visiting flies (Diptera). This dataset consists of adult fly life history information extracted from reviewed articles, such as the feeding mechanism (e.g., chewing decaying animal flesh, sucking blood, etc.), habitat, and feeding substrate of specific crop flower-visiting fly species. The quality of this extracted information is placed in two categories ('Validated in experiment', or 'Inferred (by authors)'). Chapter 2.3: A review of the life history needs of the larval and adult stages of crop flower-visiting flies (Diptera). This dataset consists of the larval fly life history information extracted from reviewed articles, including the feeding mechanism (e.g., chewing decaying animal flesh, sucking blood, etc.), habitat, and feeding substrate of specific crop flower-visiting fly species. The quality of this extracted information is placed in four categories ('Validated in experiment', 'Inferred (by authors)', '(Validated by) Expert', and 'Unable to access'). Chapter 2.4: A review of the life history needs of the larval and adult stages of crop flower-visiting flies (Diptera). This dataset consists of the data on the biogeographic host range of the species and was extracted from species catalogues, manuals, and websites (‘References’) managed by experts in the field of Dipterology. One species may occupy more than one biogeographical region. Chapter 3: Floral visitation surveys of insect visitors of hybrid seed carrot (Daucus carota subsp. sativus) crop plants. Surveys were conducted up to three times a week during full bloom (22 November to 5 December 2021) at six sites throughout the day (05:00 to 17:00). Surveys were conducted along two, 10 m transects: one along the edge of the carrot field and an additional walk in the middle (> 30 m into the field). All transects were conducted walking slowly (1 m per minute when possible) between two rows of carrot plants (either ‘Male’ and ‘Female’ or ‘Monoecious’ and ‘Monecious’). The temperature and relative humidity was recorded using Kestrel® Drop D2 data loggers permanently deployed in a shaded location within, or nearby, all study sites. All insects were identified to the lowest taxonomic level using dichotomous keys. Chapter 4: Deploying habitat to support the immature life stages of eristaline flies (Syrphidae) in hybrid seed carrot crop agroecosystems. In a paired experimental design, two habitat pools filled with substrates (‘carrot’ and ‘soil’) intended to attract eristaline flies were deployed at 7 sites. The pools were placed between 15 November to 24 November 2021 and left to decay for 12 to 21 days. Surveys of the immature life stages (‘eggs’ and/or ‘larvae’) were identified and counted within the pools. The state of the larvae (‘first instar’, ‘second instar’, ‘third instar’, or ‘dead’) as well as the location where batches of eggs were laid within the deployed habitat were determined. Chapter 5: Effectiveness of fly and bee pollinators at pollinating hybrid carrot plants grown for seed. This dataset consists of stigmas collected after a single visit by one pollinator species. The first column is date the replicate was collected, the second column is the pollinator species, the third column is the duration of time in seconds the pollinator spent visiting the replicate, the fourth column is the number of stigmas mounted on the slide, the fifth column is the number of pollinated stigmas (at least one pollen grain touching the stigma), and the sixth column is the total number of pollen grains touching the carrot stigmas. Chapter 6: Efficiency of fly and bee pollinators at pollinating blackberry (Rubus fruticosus) and raspberry (Rubus ideaus) crop plants. This dataset consists of berries harvested after single visitation (one visit to a flower), unlimited visitation (allowed access to flowers in a small cage setting), and open pollination (scale of a farm polytunnel) treatments under field conditions. The first column is the unique pollinator ID, the second column is the pollinator species, the third column is the type of trial (‘Cage’ or ‘Field’), the fourth column is the weight of the harvested fruits, the fifth column is the number of drupelets per fruit, the sixth column is type of defect found in the fruit (’None’, ‘Progressive’, or ‘ Critical’) as per industry standards, and the seventh column explains the type of defect seen in the fruit (if any).405 73 - Some of the metrics are blocked by yourconsent settings
Conference PublicationPublication Genetic Parameters for Slaughter and Meat Traits in Ostriches(Association for the Advancement of Animal Breeding and Genetics (AAABG), 2013) ;Engelbrecht, A ;Cloete, S W P; ;van Wyk, J BHoffman, L CGenetic parameters for ostrich slaughter and meat traits were estimated to determine whether the improvement of slaughter yield through genetic selection will be possible. Live weight before slaughter, 'post mortem' weight, carcass weight, pelvic limb weight, muscle weights and fat depot weights were recorded. Abdominal and subcutaneous fat weights were highly variable, while coefficients of variation in the other traits ranged between 16 and 29%. All traits showed significant genetic variation, with estimates of heritability ranging from 0.21 to 0.34 for weight and carcass traits. Heritability estimates for individual muscle weights ranged from 0.14 to 0.43, while the genetic correlations among the individual muscle weights and with pre-slaughter live weight were all positive. The substantial variation, high and favourable genetic correlations between traits, and moderate to high heritability estimates indicate that genetic improvement in ostrich carcass traits is achievable.1997 - Some of the metrics are blocked by yourconsent settings
Journal ArticlePublication Genetic Variation, Simplicity, and Evolutionary Constraints for Function-Valued Traits(University of Chicago Press, 2015) ;Kingsolver, Joel G ;Heckman, Nancy ;Zhang, Jonathan ;Carter, Patrick A ;Knies, Jennifer L ;Stinchcombe, John RUnderstanding the patterns of genetic variation and constraint for continuous reaction norms, growth trajectories, and other function-valued traits is challenging. We describe and illustrate a recent analytical method, simple basis analysis (SBA), that uses the genetic variance-covariance (G) matrix to identify "simple" directions of genetic variation and genetic constraints that have straightforward biological interpretations. We discuss the parallels between the eigenvectors (principal components) identified by principal components analysis (PCA) and the simple basis (SB) vectors identified by SBA. We apply these methods to estimated G matrices obtained from 10 studies of thermal performance curves and growth curves. Our results suggest that variation in overall size across all ages represented most of the genetic variance in growth curves. In contrast, variation in overall performance across all temperatures represented less than one-third of the genetic variance in thermal performance curves in all cases, and genetic trade-offs between performance at higher versus lower temperatures were often important. The analyses also identify potential genetic constraints on patterns of early and later growth in growth curves. We suggest that SBA can be a useful complement or alternative to PCA for identifying biologically interpretable directions of genetic variation and constraint in function-valued traits.2130 - Some of the metrics are blocked by yourconsent settings
Conference PublicationPublication Genomic breeding values for un-genotyped individualsGenomic information is now commonly used in routine genetic evaluations. This is usually in the form of genomic breeding values (GBVs) which have a high heritability but are generally confined to those animals with genotypes. This can lead to anomalies when parents have GBVs and progeny do not. By using a single-trait genetic evaluation, GBVs can be generated for related individuals. It is most efficient to do this for genotyped individuals and their ancestors initially, and calculate mid-parent values for all other individuals. A method for approximating accuracies for the relatives' GBVs is described.2198 1 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessConference PublicationHow much extra information is gained using imputed genotype data?Genotype imputation has been discussed widely as a tool to increase the statistical power associated with genome wide association studies (GWAS) and genomic prediction. Previous studies have examined the performance of imputation by evaluating how well a validation set has been predicted. The aim of this study was to examine the amount of extra information added by utilising genotype imputation. The number of new haplotype combinations, between adjacent loci, were estimated for multiple genotype densities from an Australian Sheep dataset. In our example, using genotypes from OAR6, imputation increased the number of haplotypes for 81% of the regions when imputing from 12k to 50k. Large distances between adjacent low density markers resulted in higher numbers of new haplotypes. This also corresponded to a greater proportion of low frequency haplotypes. When imputing from HD to WGS no information was added for 50% of the regions and there was a greater proportion of haplotypes with only 1 observation. Estimating the number of new haplotypes from imputation provides an understanding about the value of imputation and can be utilised to help design of reference genotype datasets.1691 142 - Some of the metrics are blocked by yourconsent settings
DatasetPublication The importance of pollinator behaviour and heterospecific pollen deposition to crop pollination service delivery(University of New England, 2023-05-23); ; ; The dataset consists of six tabs (each referring to a data chapter of the thesis). Data related to this dataset was collected online from Scopus research database (Chapter 2), and in the field from Lake Powell, Victoria, Australia (Chapter 5), and from the East-North Coast of New South Wales, Australia (chapters 3, 4, 6, and 7). Each tab has a spreadsheet with data from each thesis research chapter, and the content of each tab is explained below:
Chapter 2: A review of honey bee (Apis mellifera L.) interactions with other pollinators. The dataset consists of information extracted from reviewed articles, such as the title of the article, the authors, the year of publication, the country in which the research was performed, the place of study (i.e., open fields, or enclosed areas like glasshouses, cages, etc.), whether the study aimed to test competition or not, whether the study found and/or discussed competition or not, the type of interaction (i.e., direct or indirect) between honey bees and other species, the main methods used to perform the research, the interacting species with honey bees, and the behaviour performed by honey bees during the interaction.
Chapter 3: Observation of birds foraging on raspberry orchards. The dataset consists of the number of instances insectivorous or nectarivorous birds were seen perched on cages containing brown blowflies, within a raspberry orchard block. The first column is the days since flies were released inside cages until birds were seen inside the same cages, column two is the number of observational hours on each day of data collection, the following four columns have the bird species name and the number of individuals of each species, and the last column is the total number of individuals.
Chapter 4: Effectiveness of brown honeyeater (Lichmera indistincta) in pollinating blueberry flowers compared to insect pollinators. The dataset consists of stigmas collected after a single visit by one pollinator species. The first column is the pollinator ID, the second column is the identification of the stigma sampled, and the last column is the number of conspecific (i.e., blueberry) pollen grains deposited.
Chapter 5: Pollen collection by honey bee hives in almond orchards. The data consists of pollen pellets removed from different hives placed in almond orchards for pollination. The first column is the almond flower abundance during the flowering season (measures were always taken from the same tree branch throughout the study period), column two is the day of data collection (11 days in total), column three is the apiary identification, column four is the hive identification, column five is the heterospecific pollen richness (number of species), column six is the abundance of heterospecific pollen, column seven is the weight of heterospecific pollen collected from each hive, column eight is the weight of almond pollen collected from each hive, column nine is the total weight.
Chapter 6: Impacts of protective nets on pollen flow in blueberry orchards. The dataset consists of analyses of pollen deposition on blueberry stigmas under different netting treatments. The first column is the blueberry plant variety stigma was sampled from, column two the orchard block identification, column three is the netting treatment (i.e., covered - block completely covered by nets, partially - block partially covered by nets with sides open, and open - no nets), column four is the week of data collection (seven weeks in total), column five is the abundance of blueberry flower within each block (measures were always taken from the same blueberry plant), column six is the conspecific pollen abundance, column seven is the heterospecific pollen abundance on the stigmas, column eight is the heterospecific pollen richness in the stigmas, column nine is the point of data collection within the orchards (i.e., edge or center), and the last column is the number of non-blueberry flowers present in the remnant vegetation surrounding the orchard blocks.
Chapter 7: Effects of multiple visits on pollen deposition in blueberry, blackberry, and raspberry flowers. The dataset consists of pollen deposition analyses after multiple visits by different insect taxa in blueberry, blackberry, and raspberry flowers. The first column is the sample identification, column two is the crop species (i.e., Rubus sp - raspberry, rabbiteye - blueberry, or blackberry), column three is the crop species variety, column four is the block identification, column five is the date of sample collection, column six is the row number within the block that the sample was collected from, column seven is the identification tag used for the sample during collection, column eight is the total number if visits received by the sample (i.e., stigma), column nine is the combination of species that visited the stigma (i.e., MX - mix of species, SB - stingless bees, HB - honey bees, CR - carpenter bees), column ten is the number of conspecific pollen counted on the stigma, column eleven is the number of heterospecific pollen counted on the stigma, column twelve is the richness of heterospecific pollen counted on the stigma, column thirteen is the total visit duration time in seconds, column fourteen to thirty four is the visit duration of each subsequent visit.
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Publication Open AccessJournal ArticleThe Influence of Predictability and Controllability on Stress Responses to the Aversive Component of a Virtual Fence(Frontiers Research Foundation, 2020-11-30); ; ; ;Belson, Sue ;Keshavarzi, Hamideh ;Mayes, BonnieTo ensure animal welfare is not compromised, virtual fencing must be predictable and controllable, and this is achieved through associative learning. To assess the influence of predictability and controllability on physiological and behavioral responses to the aversive component of a virtual fence, two methods of training animals were compared. In the first method, positive punishment training involved sheep learning that after an audio stimulus, an electrical stimulus would follow only when they did not respond by stopping or turning at the virtual fence (predictable controllability). In the second method, classical conditioning was used to associate an audio stimulus with an electrical stimulus on all occasions (predictable uncontrollability). Eighty Merino ewes received one of the following treatments: control (no training and no stimuli in testing); positive punishment training with an audio stimulus in testing (PP); classical conditioning training with only an audio stimulus in testing (CC1); and classical conditioning training with an audio stimulus followed by electrical stimulus in testing (CC2). The stimuli were applied manually with an electronic collar. Training occurred on 4 consecutive days with one session per sheep per day. Sheep were then assessed for stress responses to the cues by measuring plasma cortisol, body temperature and behaviors. Predictable controllability (PP) sheep showed no differences in behavioral and physiological responses compared with the control treatment (P < 0.05). Predictable uncontrollability of receiving the aversive stimulus (CC2) induced a higher cortisol and body temperature response compared to the control but was not different to CC1 and PP treatments. CC2 treatment sheep showed a higher number of turning behaviors (P < 0.001), and more time spent running (P < 0.001) than the control and PP treatment groups, indicating that predictability without controllability was stressful. The behavior results also indicate that predicting the event without receiving it (CC1) was less stressful than predicting the event then receiving it (CC2), suggesting that there is a cost to confirmation of uncontrollability. These results demonstrate that a situation of predictability and controllability such as experienced when an animal successfully learns to avoid the aversive component of a virtual fence, induces a comparatively minimal stress response and does not compromise animal welfare.1230 233 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessConference PublicationMildly Penalized Maximum Likelihood Estimation of Genetic Covariances Matrices Without TuningA scheme for penalized estimation of genetic covariance matrices free from tuning - using default settings for the strength or penalization - is described and its efficacy is demonstrated by simulation. Estimates of genetic covariance matrices, ΣG, are known to be afflicted by substantial sampling errors, increasing markedly with the number of traits considered. 'Regularization', i.e. modification of estimators to reduce sampling variation at the expense of a small, additional bias, has been advocated to obtain estimates closer to the population values. An early suggestion by Hayes and Hill (1981, 'bending') has been to shrink the canonical eigenvalues... towards their mean.2077 - Some of the metrics are blocked by yourconsent settings
Journal ArticlePublication Modelling urinary purine derivatives excretion as a tool to estimate microbial rumen outflow in alpacas ('Vicugna pacos')Three experiments were carried out to establish a model to estimate the forestomach microbial yield based on the urinary excretion of purine derivatives (PD: allantoin, uric acid, xanthine and hypoxantine) in alpacas ('Vicugna pacos'). In Experiment 1, endogenous PD excretion was measured in two fasted adult male alpacas for seven consecutive days. Daily urinary PD excretion (μmol/kg BW0.75) decreased during fasting to a minimum value of 194.8 (s.e. 18.4), ranging from 215.3 to 174.3. In Experiment 2, the relationship between purine bases (PB) input and urinary PD output was defined in two alpacas fitted with an infusion catheter at the terminal third compartment of the forestomach (C3). Animals were fed alfalfa hay at a maintenance level, and four RNA-doses (4.2, 8.3, 12.5 and 16.6 mmol PB/day; RNA from Torula yeast) were continuously infused at random into the C3 in four successive 120 h-periods. Urinary recovery of C3 infused purines averaged 0.615 (s.e. 0.0006) mmol/day. In Experiment 3, urinary PD response to levels of feed intake corresponding to 100, 75, 50 and 20% of the previous voluntary intake was evaluated. The amount of PD excretion in urine increased linearly (r = 0.867) with digestible organic matter intake (DOMI), and the slope of the regression (16.7 mmol PD/kg DOMI) can be assumed as an index of microbial yield.942 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessConference PublicationOn implied genetic effects, relationships and alternate allele codingThis paper examines some of the implied effects commonly assumed when building relationship matrices. We propose the inclusion of an additional 'individual' in the genomic relationship matrix which models the mean of the founder population. It is shown that this resolves the problem of inconsistent prediction error variances due to alternate allele coding schemes.2175 7 - Some of the metrics are blocked by yourconsent settings
Conference PublicationPublication On property benefits of precision livestock management technologies(AgResearch Grasslands, 2012) ;Bishop-Hurley, Greg J ;Swain, David L ;Gregg, Daniel; Petty, StevePrecision Livestock Management (PLM) has been identified as an imperative investment area in the northern Beef RD&E Strategy. Precision Livestock Management refers to a range of new technologies and applications with the potential to improve environmental sustainability, productivity, price received, labour and cost efficiency through enhanced measurement, monitoring or management. However, it is still unclear exactly what benefits incorporating these technologies into northern Australian beef enterprises would deliver. Difficulties in defining how emerging technologies could be applied and the lack of quantitative property level data on which to base assumptions about technology costs and benefits contribute to this uncertainty. The project team have been working with five commercial beef producers across northern Australia to identify how six PLM technologies can be applied at the enterprise level. The six technologies considered were: 1) walk over weighing (WOW), 2) auto-drafting, 3) the ePreg system, 4) low resolution spatial animal information, 5) high resolution spatial animal information and 6) remote vegetation sensing. The objectives of the project is to ranked the economic benefits and feasibility of promising PLM technology applications for five northern beef case-study properties and investigate how these might be implemented to measure their impact on the enterprise. The five case study properties will be located in Queensland, the Northern Territory and the Kimberley and Pilbara regions of Western Australia. PLM technologies will be evaluated in relation to the enterprise-operating environment and their potential to increase enterprise operating margin. A complete model of farm production costs and benefits was implemented to evaluate the potential economic impact from PLM technologies. In-depth interviews with case-study property managers were conducted to obtain economic and production data about the current enterprise and provide insights into the expected benefits of selected PLMs. The approach used allows property and regional level differences in potential net benefits of the PLM technologies to be captured. The economic analysis will focus on property-level potential net benefits of the selected PLM technologies using the case studies to inform a farm-business model incorporating risk and uncertainty. The method proposed represents a generalisation of traditional Benefit Cost Analysis (BCA) allowing examination of traditional BCA metrics such as the Internal Rate of Return (IRR), discounted cash flows and the Benefit Cost Ratio (BCR) cash flows, benefit cost analysis, net present value and internal rate of return.1125 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessConference PublicationOptimising bias and accuracy in genomic prediction of breeding values(Massey University, 2018) ;Gowane, G R; ; ; ;Al-Mamun, Hawlader AReference populations used for genomic selection (GS) usually involve highly selected genotyped individuals which may result in biased prediction of genomic estimated breeding values (GEBV). Bias and accuracy of GEBV in animal breeding programs was explored for various prediction methods. The data was simulated to compare Best Linear Unbiased Prediction of breeding values using pedigree based relationships (PBLUP), genomic relationships for genotyped animals only (GBLUP) and a Single Step approach (SSGBLUP), where information on genotyped individuals was used to infer realised relationship among all available genotyped and non-genotyped individuals that were linked through pedigree. In the SSGBLUP, varying weights (α=0.95, 0.50) for the genomic relationship matrix (G) relative to the A-matrix weights (1-α) were applied to construct an H matrix. Different selection and mating designs with various heritabilities (h²) and QTL models were tested to compare the methods. Results showed that the accuracy of the GEBV prediction increased linearly with an increase in the number of animals selected for genotyping in the reference data. For a random mating design with no selection (RR), all prediction methods were unbiased. Prediction bias was evident in GBLUP, when a smaller proportion was more intensely selected for genotyping but bias was smaller when the proportion of selectively genotyped animals was 20% or higher. The SSGBLUP (α=0.95) showed more accuracy compared to GBLUP and there was less bias with selective genotyping. However, PBLUP and SSGBLUP did show some bias with selection and assortative mating, probably due to not fully accounting for allele frequency changes due to selection of QTL with larger effects. This bias was larger in SSGBLUP than in PBLUP, likely due to the G- and A-matrices not being coherently scaled with allele frequency changes. SSGBLUP required lower values of α to decrease bias and increase accuracy of GEBV with selection and positive assortative mating. Models with a higher h² were more accurate and less biased in the prediction, compared to those with a lower h². Results suggest that selective genotyping in a breeding programme can lead to significant bias in prediction of GEBV when only evaluating genotyped individuals. The SSGBLUP method can provide more accurate and less biased estimates but more attention needs to be paid to appropriate scaling of A and G matrices in selected populations.2037 393 - Some of the metrics are blocked by yourconsent settings
Journal ArticlePublication PA Innovations in Livestock, Grazing Systems and Rangeland Management to Improve Landscape Productivity and SustainabilityInnovative precision agriculture (PA) technologies are increasingly being used in the plant industries whilst similar techniques and opportunities have been slow to evolve in the grazing industries. The need for improved animal production efficiency is driving many producers to evaluate the PA technologies that could be applied in grazing systems, from site specific management (SSM) of fertiliser, objective pasture biomass measurement, individual animal production assessment and automatic livestock monitoring technologies (ALMS). This paper explores some of these, including SSM, ALMS, walk-over-weigh and remote automated drafting technologies in the context of their potential value for graziers seeking to implement them.1048 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessJournal ArticlePasture diet of cattle contributes to the reproductive success of dung beetles- Cattle diet plays a crucial role in the quality of dung and the consequent reproductive capacity of dung beetles. We investigated how three pasture types (improved native, forage oat and inter-sown rye/clover) influence the dung quality, the number of broods and reproductive output measured as brood size (dry weight and ellipsoid volume), development time and F1 progeny size (beetle length and pronotum width) of Onthophagus binodis, Euoniticellus africanus and Euoniticellus intermedius.
- Nitrogen content was highest in rye/clover-derived dung compared with improved native and forage oat. Improved native-derived dung had the highest carbon, energy, organic matter, pH and insoluble non-starch polysaccharide content, whereas forage oat had the lowest contents. Forage oat had the highest moisture content, ash and soluble non-starch polysaccharide content compared with the other pastures.
- Progeny length was influenced by pasture type, with female E. intermedius, and males and females of O. binodis being 11.4%, 11.2% and 7.3% longer, respectively, in rye/clover-derived dung than forage oat dung. The pronotum width of O. binodis F1 progeny was 9.8% wider when produced from rye/clover dung than forage oat.
- Rye/clover- and improved native-derived dung provided the best resource for dung beetle reproduction compared with forage oat dung. Based on this study, cattle diet is important for consideration when evaluating reproductive ability and progeny measurements. Cattle diet should be further investigated as only three pasture types were investigated out of a numerous number of species and combinations.
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Conference PublicationPublication Penalized Estimation of Covariance Matrices with Flexible Amounts of ShrinkagePenalized maximum likelihood estimation has been advocated for its capability to yield substantially improved estimates of covariance matrices, but so far only cases with equal numbers of records have been considered. We show that a generalization of the inverse Wishart distribution can be utilised to derive penalties which allow for differential penalization for different blocks of the matrices to be estimated. However, this requires multiple tuning factors to be determined and thus can increase computational requirements markedly. Simulation results are presented which indicate that the additional gains obtainable for estimates of genetic covariance components - over and above those from a simple, non-differential scheme - are moderate, even if numbers of records for different traits differ by orders of magnitude.2058 - Some of the metrics are blocked by yourconsent settings
Conference PublicationPublication Post-Estimation Penalization: More 'PEP' for Estimates of Genetic Covariance MatricesMaximum likelihood estimation of genetic covariances subject to a penalty to reduce sampling variation has been shown to yield improved estimates, especially for analyses comprising many traits. However, this can increase computational requirements substantially. Similarly, penalties have been found to be beneficial in a maximum likelihood based approach for pooling results from analyses of subsets of traits. This paper examines the scope for using the latter method to apply penalties to results from multivariate analyses in a computationally undemanding post-estimation step. A simulation study is presented demonstrating that even slight changes to estimates in this way can result in 'regularized' values markedly closer to population values than standard, unpenalized estimates.2107 - Some of the metrics are blocked by yourconsent settings
Journal ArticlePublication Predicting lactation yields in dairy buffaloes by interpolation and multiple trait predictionMilk recording systems for dairy buffaloes in the Philippines suffer from missing or irregular fat and protein test intervals; hence a suitable method to predict lactation yield is needed. The test interval method was compared with methods that incorporate information on standard lactation curves using Wilmink's (Wil) or Wood's (Wood) function. The latter two methods were also evaluated using a multiple trait procedure with covariances between milk, fat and protein yields, MTP-Wil and MTP-Wood, for 305D yield prediction. For this purpose, 1700 lactation records of dairy buffaloes from seven herds located in the north and south of the Philippines were used. All lactations have daily milk yields and most also have monthly fat and protein test day yields. Accuracy of predicting 305D milk, fat and protein yields were evaluated using ≥9 test day yields (≥9TD) of complete lactations, part lactation of varying lengths and lactations with missing tests with varying intervals between tests. The five methods were compared based on mean squared error and correlation between the predicted and true 305D yield. Prediction of 305D milk and protein yields was equally precise among the five methods when ≥9 test day yields were used. In general, MTP-Wil had slightly better precision compared with TIM and Wil methods in extending part lactations to 305D yields for all 3 traits. The use of Wood's function to model the lactation curve resulted in large prediction error when extending yields to 305D from short lactations. The methods, MTP-Wil and MTP-Wood, which utilize information on covariances between traits had slightly better performance and are able to handle missing tests and longer intervals between tests better than other methods. Fat and protein 305D yields can be predicted using a single test with almost similar accuracy using ≥9TD yields provided that complete milk test day information is available. Overall, MTP-Wil performed better than the other methods and is more applicable in situations where missing tests or irregular test intervals are frequently encountered in milk recording system.1036 1 - Some of the metrics are blocked by yourconsent settings
BookPublication Primer to Analysis of Genomic Data Using RThrough this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto.2365 - Some of the metrics are blocked by yourconsent settings
Journal ArticlePublication Random regression test day models to estimate genetic parameters for milk yield and milk components in Philippine dairy buffaloesHeritabilities and genetic correlations for milk production traits were estimated from first-parity test day records on 1022 Philippine dairy buffalo cows. Traits analysed included milk (MY), fat (FY) and protein (PY) yields, and fat (Fat%) and protein (Prot%) concentrations. Varying orders of Legendre polynomials (Legm) as well as the Wilmink function (Wil) were used in random regression models. These various models were compared based on log likelihood, Akaike's information criterion, Bayesian information criterion and genetic variance estimates. Six residual variance classes were sufficient for MY, FY, PY and Fat%, while seven residual classes for Prot%. Multivariate analysis gave higher estimates of genetic variance and heritability compared with univariate analysis for all traits. Heritability estimates ranged from 0.25 to 0.44, 0.13 to 0.31 and 0.21 to 0.36 for MY, FY and PY, respectively. Wilmink's function was the better fitting function for additive genetic effects for all traits. It was also the preferred function for permanent environment effects for Fat% and Prot%, but for MY, FY and PY, the Legm was the appropriate function. Genetic correlations of MY with FY and PY were high and they were moderately negative with Fat% and Prot%. To prevent deterioration in Fat% and Prot% and improve milk quality, more weight should be applied to milk component traits.957 1 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessConference PublicationA rapid method for the identification of epistatic 'dormant' SNPs(Massey University, 2018) ;Reverter, A ;Henshall, J ;Porto-Neto, L R ;Raidan, F ;Li, Y ;Naval-Sanchez, M; ;Lehnert, S A; ;Vitezica, ZLegarra, AWe present a unique computational approach for the identification of epistatic SNPs based on SNPs with significant yet opposed effects depending on the genetic background. We introduce the mechanical heuristics of the approach based on first, binning the population according to their genomic-estimated breeding value (GEBV) and second, performing genome-wide association studies (GWAS) within each bin. SNPs are deemed to be epistatic if significant but with different signed effects in the GWAS from the most extreme bins containing individuals with the lowest and highest GEBV. We then show that these heuristics are equivalent to a regression of residuals on GEBV. Next, we illustrate our approach with a dataset of 2,111 cattle genotyped for 651,253 SNPs and using yearling weight as the phenotype. We identify 243 epistatic SNPs, and argue that these SNPs are 'dormant' with an additive effect waiting to be 'released' if selection moves the population to either tail of the genetic value distribution.2398 7 - Some of the metrics are blocked by yourconsent settings
Publication Open AccessConference PublicationRealising Genetic Improvement for the Extensive Livestock Industries as a WholeThis paper examines some aspects of the overall performance of livestock improvement systems, first asking what we mean by the term "system". Variation in behaviour of agents within the system is examined, and some tentative conclusions about the nature of such systems, and scope for their management, proposed.2399 - Some of the metrics are blocked by yourconsent settings
Conference PublicationPublication Sampling Based Approximation of Confidence Intervals for Functions of Genetic Covariance Matrices(Association for the Advancement of Animal Breeding and Genetics (AAABG), 2013); Houle, DavidApproximate lower bound sampling errors of maximum likelihood estimates of covariance components and their linear functions can be obtained from the inverse of the information matrix. For non-linear functions, sampling variances are commonly determined as the variance of their first order Taylor series expansions. This is used to obtain sampling errors for estimates of heritabilities and correlations, and these quantities can be computed with most software performing such analyses. In other instances, however, more complicated functions are of interest or the linear approximation is difficult or inadequate. A pragmatic alternative then is to evaluate sampling characteristics by repeated sampling of parameters from their asymptotic, multivariate normal distribution, calculating the function(s) of interest for each sample and inspecting the distribution across replicates. This paper demonstrates the use of this approach and examines the quality of approximation obtained.2188