A study on some aspects of the pathogenicity, diagnosis and control of gastrointestinal nematodes in deer : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand

The most important parasites in farmed red deer are Dictyocaulus eckerti and gastrointestinal nematodes (GIN). The overall aim of these studies was to develop an understanding about GIN parasites in red deer, including their pathogenicity, diagnosis, control and the risk of cross-infection with cattle/sheep. To understand the pathogenicity of GIN, young deer were trickle infected with a mixed culture of deerorigin infective larvae (L3). The infection comprised 40% Ostertagia-type and 53% Oesophagostomum spp. L3. As a result of the high proportion of Oesophagostomum spp. L3, the animals were clinically affected with large intestinal lesions and it was not possible to investigate the effect of Ostertagia-type parasites. Oesophagostomum sikae was recognised in New Zealand for the first time in this study. A national survey of the prevalence of different GIN in deer utilised PCR-based methodology. From each of 59 deer farms around New Zealand faeces from an average of 19 deer/farm were cultured and 24 infective larvae were randomly selected and identified. The order of prevalence from high to low was Oesophagostomum. venulosum > Spiculopteragia asymmetrica > S. spiculoptera > Ostertagia leptospicularis. This illustrated the importance of abomasal nematodes in the subfamily Ostertaginae. A study was conducted to determine the ability of sheep GIN to establish in deer. The highest establishment rates were Haemonchus contortus (10.5%), Trichostrongylus axei (12.2%) and O. venulosum (5.8%). However, these were all lower than in sheep. The effectiveness of crossgrazing system between deer and sheep (DS) or cattle (DC) compared to deer grazing alone (DD) was undertaken as a replicated study at two locations over two years. The key outcomes were that DC needed fewer anthelmintic treatments and still had higher live-weight than other groups. The DD group received more treatments and still had highest nematode counts for Ostertagia-type nematodes and Dictyocaulus. The DS group received a similar number of treatments to DD and had the highest burdens of T. axei. Cross-grazing offers advantages which varied between DC and DS with regards the level of control of GIN, however, both were effective in controlling lungworm infection. Deer in all groups still required anthelmintic treatment to maintain growth rates

Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment

The blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve species supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical–chemical ocean farming conditions. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis of M. chilensis and M. coruscus was conducted, revealing genic rearrangements distributed into the whole genome. Notably, transposable Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. The evidence suggests that local genome adaptation and physiological plasticity can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex

Introduced deer and their potential role in disease transmission to livestock in Australia

1. The transmission of pathogens between wildlife and livestock is a globally recognised threat to the livestock industry, as well as to human and wildlife health. Wild cervids are susceptible to many diseases affecting livestock. This presents a challenge for wildlife and domestic animal disease management because the frequent use of agricultural areas by wild cervids may hamper the effectiveness of disease control strategies. 2. Six deer species have established wild populations in Australia and are expanding in range and abundance. A comprehensive literature review of diseases impacting deer and livestock was undertaken, resulting in consideration of 38 pathogens. A qualitative risk assessment was then carried out to assess the overall risk posed by the pathogens to the livestock industry. 3. Five diseases (bovine tuberculosis, foot and mouth disease, malignant catarrhal fever, surra, and screw‐worm fly infestation) ranked highly in our risk assessment. Of these five diseases, only one (malignant catarrhal fever) is currently present in Australia, but all five are notifiable diseases at a national level. Data on these diseases in deer are limited, especially for one of the most abundant species, the sambar deer Rusa unicolor, highlighting a further potential risk attributable to a lack of understanding of disease epidemiology. 4. This paper provides a detailed review of the pathogens affecting both cervids and livestock in Australia, and applies a qualitative framework for assessing the risk posed by deer to the livestock industry. The qualitative framework used here could easily be adapted to assess disease risk in other contexts, making this work relevant to scientists and wildlife managers, as well as to livestock industry workers, worldwide