Cattle are essential for the global food industry through the meat and milk production. It is from an economical point of view in our best interest to make cattle as efficient as possible, whether it is milk or beef production, without negatively influencing their health and welfare. That has led to a steady increase in the interest of genetic analysis of cattle. The sequencing and identification of genomic variation has led to the association of genotypes with phenotypes of interest and the discovery of the underlaying genetic risk factors for many diseases and traits. Diseases or monogenetic traits caused by a single nucleotide polymorphism (SNP), small deletions and insertions or other small mutations are often easy to identify if the correct region is found. The diseases caused by structural variants (SVs), variants larger than 50 base pairs (bp) are still challenging. It is more challenging because they are harder to identify, especially using shortread sequencing technologies. It is therefore still a rather unexplored area for cattle and other domestic species.This thesis looks at SVs found in the Swedish Red and Brown (SRB) cattle to discover breed specific SVs. This was done by creating a pipeline with VCF files as input. The identified SVs were filtered and overlapped with externally identified SVs. The pipeline was tested with two SRB datasets. The structural variant caller, DELLY, performed poorly with low read depth data when comparing single replicate data and combined replicates data. Multiple SVs were identified in all individuals and did overlap with both functional and gene annotation. There was also overlap found with datasets in the European variant archive (EVA). This indicates that the identified SVs are shared among multiple breeds of cattle and that DELLY can be used to develop future pipelines to include long read sequencing technologies and/or data with higher read depth.

The dog brings great joy and is of great benefit to humans, for example as a companion dog, hunting dog, service dog and assistance dog. In some cases, dogs cause problems and society must then intervene. The Act of Supervision of Dogs and Cats aims at preventing damage and significant inconvenience that can be caused by dogs and cats. If a dog causes damage or nuisance according to The Act of Supervision of Dogs and Cats, the law can support a decision to seize a dog by the County Administrative Board or the Police Authority. Often the dog is seized because it has bitten another dog, human or other animal. In case of seizure, an investigation must be carried out by the County Administrative Board to assess the dog's mental and physical status. The Police inspector performs a mental examination of the dog, and a Veterinarian examines the dog's physical status. The County Administrative Board then decides whether the dog should be returned to its owner, rehomed, or euthanized. This study has examined the county administrations' work in Norrbotten, Skåne, Stockholm, Västerbotten, Västmanland and Västra Götaland. A total of 89 dogs were seized in the six counties, between the years 2019–2021, 53 male dogs (approx. 60%) and 36 female dogs (approx. 40%). Euthanasia was the most frequently performed measure, 42 dogs were euthanized. Others were returned or rehomed. In general, all six county administrations carry out careful investigations, but a clear difference between them is how often the county administrations follow the police's proposed measures. The county administrative boards decide on euthanasia more often, 42 out of 89 times (47%), than the police give suggestions on euthanasia, 34 out of 89 times (38%). The new regulation, which entered into force on February 1, 2022, makes it possible for the county administrations to be even more thorough in their investigations of dogs in care. In addition to a mental examination and veterinary examination, the county administrations must also request a statement from the kennel about the dog's behaviour towards people and animals. / Hunden ger stor glädje och gör stor nytta för människan, exempelvis som sällskapshund, jakthund, tjänstehund och assistanshund. I enstaka fall orsakar hundar problem och samhället måste då ingripa. Lagen (2007:1150) om tillsyn över hundar och katter, härefter ”TL” eller ”tillsynslagen” finns för att förebygga skador och avsevärda olägenheter som kan orsakas av hund och katt. Om en hund orsakar skada eller olägenhet enligt TL kan hunden omhändertas av länsstyrelse eller Polismyndigheten. Ofta blir hunden omhändertagen för att den har bitit en annan hund, människa eller annat djur.  Vid ett omhändertagande ska en utredning genomföras av länsstyrelsen för att bedöma hundens psykiska- och fysiska status. Besiktningsman på polisen gör en mentalbesiktning av hunden och veterinär granskar hundens fysiska status. Därefter tar länsstyrelsen beslut om hunden ska återlämnas till sin ägare, omplaceras eller avlivas. I denna studie har länsstyrelserna arbete i Norrbotten, Skåne, Stockholm, Västerbotten, Västmanland och Västra Götaland granskats. Totalt omhändertogs 89 hundar i de sex länen, 2019–2021, 53 hanhundar (ca 60 %) och 36 tikar (ca 40 %). Avlivning var den åtgärd som utfördes oftast, 42 hundar avlivades. Övriga återlämnades eller omplacerades. Länsstyrelserna beslutar oftare om avlivning, 42 av 89 gånger (47 %), än vad polisen ger förslag om avlivning, 34 av 89 gånger (38 %). Generellt gör alla sex länsstyrelserna gedigna utredningar men det som framför allt skiljer dem åt är hur ofta respektive länsstyrelse följer polisens förslag på åtgärd. Den nya föreskriften som trädde i kraft 1 februari 2022 gör det möjligt för länsstyrelserna att bli ännu mer noggranna i sina utredningar av omhändertagna hundar. Utöver mentalbesiktning och veterinärundersökning ska länsstyrelserna även begära utlåtande från uppstallningsplatsen, om hundens beteende mot människor och djur.

The aim of this study was to investigate how the crime of animal cruelty is constructed and what lies behind these crimes where animals have been suffering.The study's data consisted of 76 animal cruelty judgements, the verdict pronounced between January 2017 and December 2018. Animal cruelty occurred in all of Sweden's counties. Most of the crimes were committed by perpetrators in the age group 50-59 years and men committed more crimes than women. Most of the crimes (92%) also resulted in day fines, which were combined with a suspended sentence in 63% of the cases. In 90% of the cases the day fines were for an amount of SEK 200 or less, and 43% of the perpetrators were given a suspended sentence or day fines of a minimum amount (SEK 50).Neglect concerning the primary lack of care, was the most common crime category (77% of all cases). Dogs were the most frequently affected species within both cases of neglect (39%) as well as in cases of abuse (79%), which is in line with previous studies regarding animal cruelty crimes. Men accounted for 92% of the cases in the crime category of abuse and women accounted for 49% of the cases in the category of neglect. In 40% of the judgments where cats were involved, the animal keeper also kept several other types of animals or had a larger total number of animals (68 animals at most), which may indicate animal hoarding. In almost half of the investigated cases, animals had either died or had to be euthanized because of the crime. It also turned out that some of the perpetrators violated an existing animal ban and nearly 15% of the crimes resulted in new animal bans. Approximately 15% of the judgements indicate animal hoarding and the lack of cooperation between authorities. It also appears that animal bans are not always complied by those who are imposed with the ban and further measures are therefore required for the ban to be complied with. Animal cruelty needs to be studied further and whether the new law on grave animal cruelty turns out to have the intended effect in practice. / Syftet med denna studie var att undersöka hur brottet djurplågeri är konstruerat och vad som ligger bakom dessa brott där djur blivit lidande. Studiens dataunderlag bestod av 76 djurplågeridomar som meddelats mellan januari 2017 och december 2018. Djurplågeri förekom i Sveriges samtliga län. Flest brott begicks av personer i åldersgruppen 50–59 år och män begick fler brott än kvinnor. Merparten av brotten (92 %) ledde till dagsböter, som i 63 % av fallen förenades med en villkorlig dom. I 90 % av fallen låg dagsböterna på 200 kronor eller mindre och 43 % av gärningspersonerna fälldes för brottet med en villkorlig dom eller dagsböter av minimibelopp (50 kr). Vanvård i form av primära skötselbrister var den vanligaste brottstypen (77 % av fallen) och hundar var det djurslag som drabbades oftast i såväl vanvårdsfall (39 %) som misshandelsfall (79 %), vilket är i linje med tidigare studier avseende djurplågeri. Männen stod för 92 % av brottstypen misshandel och kvinnor 49 % inom brottstypen vanvård. I 40 % där djurslaget katt förekom, höll djurhållaren flera olika djurslag men i flera fall även ett stort antal djur (som mest 68 stycken djur), vilket kan tyda på ett tvångsmässigt djursamlande. I närmare hälften av de undersökta domarna hade djur antingen självdött eller behövt avlivas på grund av brottet. Det visade sig även att en del av gärningspersonerna överträtt befintligt djurförbud och närmare 15 % av brotten resulterade i nya djurförbud. Omkring 15% av domarna tyder på djursamlande och ett bristande samarbete mellan myndigheter. Det framkommer även att djurförbud inte alltid efterlevs och att ytterligare åtgärder krävs för att förbudet ska efterlevas. Djurplågeri behöver studeras vidare och om den nya lagen om grovt djurplågeri visar sig få avsedd effekt i praktiken.

Domesticated species possess certain cognitive abilities that allow them to thrive in an environment with regular human interaction, and these interactions contribute to the overall human-animal relationship. Studying the human-animal relationship allows us to better understand how domesticated animals perceive and navigate their environment, which can then be used to improve their welfare. In chickens, this relationship is poorly understood, and further research would provide insight into the welfare needs of this animal. Here we show breed differences in the interspecific sociocognitive abilities of Gallus gallus, where the domesticated White Leghorn interacted more with a familiar human than the red junglefowl, and both the domesticated White Leghorn and the red junglefowl breed that had been selected for low fear of humans were habituated to human presence. This study sheds light on the effect of domestication on social cognition in chickens and begins to describe the human-chicken relationship.

An optimal method for stunning animals before slaughter should result in instantaneous and irreversible insensibility. Today, there are various stunning and slaughter practices used around the world for farmed fish. With aquaculture being a growing food sector, the welfare of the animals used has become increasingly important in the consciousness of consumers, researchers and regulatory bodies. With growing research into the subject matter, an overview to summarize and examine how these practices impact on the welfare of the fish, and how well they conform to animal welfare legislation, is warranted to minimize the suffering of farmed fish. Stunning practices used in aquaculture include methods such as electrical and percussive stunning, carbon dioxide and asphyxiation. Each with its own level of effectiveness in terms of how fast the method results in loss of consciousness, whether or not the effect is reversible and how the welfare of the fish is affected as determined by behavioural and physiological stress responses. It was concluded that there is no unambiguous answer as to which stunning method is optimal in regard to animal welfare in modern day aquaculture. The optimal method for a given facility is influenced by factors like practicalities relating to each individual method as well as legislation on EU and national level. Suggestions were made for future research.

The research presented in this thesis focuses on an innovative use of digital imaging, and the machine learning techniques to assess the body rumen fill scoring in dairy cows. This study aims to enhance the efficiency of monitoring and managing dairy cow health, which is crucial for the dairy industry's productivity and sustainability. The primary objective was to develop an automated annotation system fore valuating rumen fill status in dairy cows using digital images extracted from recorded videos. This system leverages advanced machine learning algorithms and neural networks, aiming to mimic manual assessments by veterinarians and specialists on farms. To achieve the above objectives, this thesis made use of already existing video records from a Swedish dairy farm hosting mainly the Swedish Redand the Swedish Holstein breeds. A subset of these images were then processed, manually classified using a modified rumen fill scoring system based on visual assessment, and supervised classification algorithms were trained on 277 manually annotated images. The thesis explored various machine learning techniques for classifying these images, including Logistic Regression, Support Vector Machine (SVM), and a Deep Neural Network using the VGG16 architecture. These models were trained, validated, and tested with a dataset that included variations in cow color patterns, aiming to determine the most effective approach for automated rumen fill scoring.The results indicated that while each model had its strengths and weaknesses, the simple logistic model was performing the best in terms of test accuracy and F1 score. This research contributes to the field of precision livestock farming, particularly in the context of dairy farming. By automating the process of rumen fill scoring, the study aims to provide dairy farmers with a reliable, efficient, and cost-effective tool for monitoring cow health. This tool has the potential to enhance dairy cow welfare, improve milk production, and support the sustainability of dairy farming operations. However, at the current state, the model accuracy of the best model was only moderate. There is a need for further improvement of the prediction performance possibly by adding more cow images, using improved image processing, and feature engineering.

Den domesticerade kaninen (Oryctolagus cuniculus) är idag ett vanligt sällskapsdjur världen över. Sällskapskaniner framhålls som det tredje mest populära sällskapsdjuret i Sverige, efter hund och katt. Trots detta behandlar endast en mycket liten andel av den övergripande forskningen inom ämnet hälsa- och välfärd just kanin. Den här studien har undersökt inverkan på sällskapskaninens välfärd av kaninägare med eller utan tidigare erfarenhet, sjukdomsbild, samt kaninägares preferenser - och om detta är faktorer som påverkar sällskapskaninens välfärd i Sverige. Studien genomfördes som en enkätundersökning, besvarad av 147 deltagare bosatta i Sverige. Enkäten publicerad i nätverkstjänsten Facebook och fanns tillgänglig under tidsperioden 23:e April - 7:e Maj, 2021. Mer än 50 % av deltagarna saknade erfarenhet och kunskap om kaniner innan de skaffade sin första kanin. Över 37 % höll sina kaniner ensamlevande, och mer än 21 % inhyste sina kaniner i bur. Behovet av veterinärvård utgjordes totalt av nästan hälften av kaninerna, och de kaniner som hölls inomhus eller frigående hade störst behov. Det fanns en skillnad i behovet av veterinärvård hos olika raskategorier, där kategorin små raser var högst representerad. Antalet kaniner som drabbades av olika typer av hälsorelaterade problem varierade, men sjukdomar kopplade till avelsrelaterad problematik utgjordes av nästan 1/3 av alla sjukdomar. Den vanligaste raskategorin att hålla var dvärgraser som hölls av nästan 60 % av alla deltagare, och den vanligaste orsaken till att välja just den raskategorin utgjordes av dess storlek. Den här studien visade att det finns faktorer i kaninägarens djurhållning som kan kopplas till sällskapskaninens välfärd i Sverige. Avgörande parametrar till detta har lyfts fram som kaninägarens erfarenhet och kunskap om kaniner, hållning och inhysning, samt val av raskategori. Nyckelord: Oryctolagus cuniculus, sällskapskanin, djurhållning, djurvälfärd, djuravel, djuretik / The domesticated rabbit (Oryctolagus cuniculus) is today a common pet worldwide. Pet rabbits are highlighted as the third most popular pet in Sweden, after dogs and cats. Despite this, only a very small proportion of the overall research in the subject of health and welfare deals with rabbits. This study has examined the impact on the companion rabbit's welfare of rabbit owners with or without previous experience, disease picture, and rabbit owners' preferences - and whether these are factors that affect the companion rabbit's welfare in Sweden. The study was conducted as a survey, answered by 147 participants living in Sweden. The survey was published in the network service Facebook and found available during the period 23 April - 7 May, 2021. More than 50% of the participants lacked experience and knowledge about rabbits before acquiring their first rabbit. Over 37% kept their rabbits alone, and more than 21% housed their rabbits in cages. The need for veterinary care accounted for a total of almost half of the rabbits, and the rabbits kept indoors or free-running were most in need. There was a difference in the need for veterinary care in different breed categories, where the category small breeds was most represented. The number of rabbits suffering from various types of health-related problems varied, but diseases linked to breeding-related problems accounted for almost 1/3 of all diseases. The most common breed category to keep was dwarf breeds held by almost 60% of all participants, and the most common reason for choosing that particular breed category was its size. This study showed that there are factors in the rabbit owner's animal husbandry that can be linked to the companion rabbit's welfare in Sweden. Decisive parameters for this have been highlighted as the rabbit owner's experience and knowledge of rabbits, posture and housing, as well as the choice of breed category. Keywords: Oryctolagus cuniculus, companion rabbit, animal husbandry, animal welfare, animal breeding, animal ethics