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Marina, H., Ren, K., Hansson, I., Fikse, F., Nielsen, P. P. & Rönnegård, L. (2024). New insight into social relationships in dairy cows, and how time of birth, parity and relatedness affect spatial interactions later in life. Journal of Dairy Science, 107(2), 1110-1123
Open this publication in new window or tab >>New insight into social relationships in dairy cows, and how time of birth, parity and relatedness affect spatial interactions later in life
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2024 (English)In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 107, no 2, p. 1110-1123Article in journal (Refereed) Published
Abstract [en]

Social interactions between cows play a fundamental role in the daily activities of dairy cattle. Real-time location systems provide on a continuous and automated basis information about the position of individual cows inside barns, offering a valuable opportunity to monitor dyadic social contacts. Understanding dyadic social interactions could be applied to enhance the stability of the social structure promoting animal welfare and to model disease transmission in dairy cattle. This study aimed to identify the impact of different cow characteristics on the likelihood of the formation and persistence of social contacts in dairy cattle. The individual position of the lactating cows was automatically collected once per second for 2 weeks, using an ultra-wideband system on a Swedish commercial farm consisting of nearly 200 dairy cows inside a free-stall barn. Social networks were constructed using the position data of 149 cows with available information on all characteristics during the study period. Social contacts were considered as a binary variable indicating whether a cow pair was within 2.5 m of each other for at least 10 min per day. The role of cow characteristics in social networks was studied by applying separable temporal exponential random graph models. Our results revealed that cows of the same parity interacted more consistently, as well as those born within 7 d of each other or are closely related by pedigree. The repeatability of the topological parameters indicated a consistent short-term stability of the individual animal roles within the social network structure. Additional research is required to elucidate the underlying mechanisms governing the long-term evolution of social contacts among dairy cattle and to investigate the relationship between these networks and the transmission of diseases in the dairy cattle population.

Keywords
animal behavior, animal welfare, precision livestock farming, social network analyses
National Category
Animal and Dairy Science
Identifiers
urn:nbn:se:du-46997 (URN)10.3168/jds.2023-23483 (DOI)37709047 (PubMedID)2-s2.0-85183575705 (Scopus ID)
Available from: 2023-09-19 Created: 2023-09-19 Last updated: 2024-02-05Bibliographically approved
Hansson, I., Silvera, A., Ren, K., Woudstra, S., Skarin, A., Fikse, W. F., . . . Rönnegård, L. (2023). Cow characteristics associated with the variation in number of contacts between dairy cows. Journal of Dairy Science, 106(4), 2685-2699
Open this publication in new window or tab >>Cow characteristics associated with the variation in number of contacts between dairy cows
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2023 (English)In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 106, no 4, p. 2685-2699Article in journal (Refereed) Published
Abstract [en]

In modern freestall barns where large groups of cows are housed together, the behavior displayed by herd mates can influence the welfare and production of other individuals. Therefore, understanding social interactions in groups of dairy cows is important to enhance herd management and optimize the outcomes of both animal health and welfare in the future. Many factors can affect the number of social contacts in a group. This study aimed to identify which characteristics of a cow are associated with the number of contacts it has with other group members in 2 different functional areas (feeding and resting area) to increase our understanding of the social behavior of dairy cows. Inside 2 herds housed in freestall barns with around 200 lactating cows each, cow positions were recorded with an ultra-wideband real-time location system collecting all cows' positions every second over 2 wk. Using the positioning data of the cows, we quantified the number of contacts between them, assuming that cows spending time in proximity to one another (within a distance of 2.5 m for at least 10 min per day) were interacting socially. We documented in which barn areas these interactions occurred and used linear mixed models to investigate if lactation stage, parity, breed, pregnancy status, estrus, udder health, and claw health affect the number of contacts. We found variation in the number of contacts a cow had between individuals in both functional areas. Cows in later lactation had more contacts in the feeding area than cows in early lactation. Furthermore, in one herd, higher parity cows had fewer contacts in the feeding area than first parity cows, and in the other herd, cows in third parity or higher had more contacts in the resting area. This study indicates that cow characteristics such as parity and days in milk are associated with the number of contacts a cow has daily to its herd mates and provides useful information for further research on social interactions of dairy cows.

Keywords
dairy cow, real-time location system, social interactions
National Category
Animal and Dairy Science
Identifiers
urn:nbn:se:du-45522 (URN)10.3168/jds.2022-21915 (DOI)000968993100001 ()36823010 (PubMedID)2-s2.0-85148870118 (Scopus ID)
Available from: 2023-02-28 Created: 2023-02-28 Last updated: 2023-05-12Bibliographically approved
Marjanovic, J., Mulder, H. A., Rönnegård, L., de Koning, D.-J. -. & Bijma, P. (2022). Capturing indirect genetic effects on phenotypic variability: Competition meets canalization. Evolutionary Applications, 15(4), 694-705
Open this publication in new window or tab >>Capturing indirect genetic effects on phenotypic variability: Competition meets canalization
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2022 (English)In: Evolutionary Applications, E-ISSN 1752-4571, Vol. 15, no 4, p. 694-705Article in journal (Refereed) Published
Abstract [en]

Phenotypic variability of a genotype is relevant both in natural and domestic populations. In the past two decades, variability has been studied as a heritable quantitative genetic trait in its own right, often referred to as inherited variability or environmental canalization. So far, studies on inherited variability have only considered genetic effects of the focal individual, that is, direct genetic effects on inherited variability. Observations from aquaculture populations and some plants, however, suggest that an additional source of genetic variation in inherited variability may be generated through competition. Social interactions, such as competition, are often a source of Indirect Genetic Effects (IGE). An IGE is a heritable effect of an individual on the trait value of another individual. IGEs may substantially affect heritable variation underlying the trait, and the direction and magnitude of response to selection. To understand the contribution of IGEs to evolution of environmental canalization in natural populations, and to exploit such inherited variability in animal and plant breeding, we need statistical models to capture this effect. To our knowledge, it is unknown to what extent the current statistical models commonly used for IGE and inherited variability capture the effect of competition on inherited variability. Here, we investigate the potential of current statistical models for inherited variability and trait values, to capture the direct and indirect genetic effects of competition on variability. Our results show that a direct model of inherited variability almost entirely captures the genetic sensitivity of individuals to competition, whereas an indirect model of inherited variability captures the cooperative genetic effects of individuals on their partners. Models for trait levels, however, capture only a small part of the genetic effects of competition. The estimation of direct and indirect genetic effects of competition, therefore, is possible with models for inherited variability but may require a two-step analysis. © 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022
Keywords
canalization, competition, IGE, indirect genetic effects, inherited variability, statistical models
National Category
Ecology
Identifiers
urn:nbn:se:du-40863 (URN)10.1111/eva.13353 (DOI)000765749600001 ()2-s2.0-85126020494 (Scopus ID)
Available from: 2022-03-22 Created: 2022-03-22 Last updated: 2023-10-24Bibliographically approved
Chozas, A., Mahjani, B. & Rönnegård, L. (2022). Family history of breast cancer is associated with elevated risk of prostate cancer: evidence for shared genetic risks. Human Heredity, 87, 12-19
Open this publication in new window or tab >>Family history of breast cancer is associated with elevated risk of prostate cancer: evidence for shared genetic risks
2022 (English)In: Human Heredity, ISSN 0001-5652, E-ISSN 1423-0062, Vol. 87, p. 12-19Article in journal (Refereed) Published
Abstract [en]

Introduction: Although breast and prostate cancers arise in different organs and are more frequent in the opposite sex, multiple studies have reported an association between their family history. Analysis of single nucleotide polymorphism data, based on distant relatives, has revealed a small positive genetic correlation between these cancers explained by common variants. The estimate of genetic correlation based on close relatives reveals the extent to which shared genetic risks are explained by both common and rare variants. This estimate is unknown for breast and prostate cancer. Method: We estimated the relative risks, heritability, and genetic correlation of breast cancer and prostate cancer, based on the Minnesota Breast and Prostate Cancer Study, a family study of 141 families ascertained for breast cancer. Results: Heritability of breast cancer was 0.34 (95% credible interval: 0.23-0.49) and 0.65 (95% credible interval: 0.36-0.97) for prostate cancer, and the genetic correlation was 0.23. In terms of odds ratios, these values correspond to a 1.3 times higher odds of breast cancer among probands, given that the brother has prostate cancer. Conclusion: This study shows the inherent relation between prostate cancer and breast cancer; an incident of one in a family increases the risk of developing the other. The large difference between estimates of genetic correlation from distant and close relatives, if replicated, suggests that rare variants contribute to the shared genetic risk of breast and prostate cancer. However, the difference could steam from genotype-by-family effects shared between the two types of cancers. ©; 2021 The Author(s).

Place, publisher, year, edition, pages
S. Karger AG, 2022
Keywords
Breast cancer, Genetic correlation, Heritability, MCMCglmm, Prostate cancer
National Category
Cancer and Oncology
Identifiers
urn:nbn:se:du-39398 (URN)10.1159/000521215 (DOI)000779059500002 ()2-s2.0-85123363092 (Scopus ID)
Available from: 2022-02-07 Created: 2022-02-07 Last updated: 2023-04-14Bibliographically approved
Ren, K., Alam, M., Nielsen, P. P., Gussmann, M. & Rönnegård, L. (2022). Interpolation Methods to Improve Data Quality of Indoor Positioning Data for Dairy Cattle. Frontiers in Animal Science, 3, Article ID 896666.
Open this publication in new window or tab >>Interpolation Methods to Improve Data Quality of Indoor Positioning Data for Dairy Cattle
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2022 (English)In: Frontiers in Animal Science, E-ISSN 2673-6225, Vol. 3, article id 896666Article in journal (Refereed) Published
Abstract [en]

Position data from real-time indoor positioning systems are increasingly used for studying individual cow behavior and social behavior in dairy herds. However, missing data challenges achieving reliable continuous activity monitoring and behavior studies. This study investigates the pattern of missing data and alternative interpolation methods in ultra-wideband based real-time indoor positioning systems in a free-stall barn. We collected 3 months of position data from a Swedish farm with around 200 cows. Data sampled for 6 days from 69 cows were used in subsequent analyzes to determine the location and duration of missing data. Data from 20 cows with the most reliable tags were selected to compare the effects of four different interpolation methods (previous, linear interpolation, cubic spline data interpolation and modified Akima interpolation). By comparing the observed data with the interpolations of the simulated missing data, the mean error distance varied from around 55 cm, using the previously last observed position, to around 17 cm for modified Akima. Modified Akima interpolation has the lowest error distance for all investigated activities (rest, walking, standing, feeding). Larger error distances were found in areas where the cows walk and turn, such as the corner between feeding and cubicles. Modified Akima interpolation is expected to be useful in the subsequent analyses of data gathered using real-time indoor positioning systems.

National Category
Animal and Dairy Science
Identifiers
urn:nbn:se:du-44343 (URN)10.3389/fanim.2022.896666 (DOI)
Funder
Swedish Research Council Formas, 2019-02111Swedish Research Council Formas, 2019-02276Kjell and Marta Beijer Foundation
Available from: 2022-12-15 Created: 2022-12-15 Last updated: 2023-03-17Bibliographically approved
Stingo-Hirmas, D., Cunha, F., Cardoso, R. F., Carra, L. G., Rönnegård, L., Wright, D. & Henriksen, R. (2022). Proportional Cerebellum Size Predicts Fear Habituation in Chickens. Frontiers in Physiology, 13, Article ID 826178.
Open this publication in new window or tab >>Proportional Cerebellum Size Predicts Fear Habituation in Chickens
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2022 (English)In: Frontiers in Physiology, E-ISSN 1664-042X, Vol. 13, article id 826178Article in journal (Refereed) Published
Abstract [en]

The cerebellum has a highly conserved neural structure across species but varies widely in size. The wide variation in cerebellar size (both absolute and in proportion to the rest of the brain) among species and populations suggests that functional specialization is linked to its size. There is increasing recognition that the cerebellum contributes to cognitive processing and emotional control in addition to its role in motor coordination. However, to what extent cerebellum size reflects variation in these behavioral processes within species remains largely unknown. By using a unique intercross chicken population based on parental lines with high divergence in cerebellum size, we compared the behavior of individuals repeatedly exposed to the same fear test (emergence test) early in life and after sexual maturity (eight trials per age group) with proportional cerebellum size and cerebellum neural density. While proportional cerebellum size did not predict the initial fear response of the individuals (trial 1), it did increasingly predict adult individuals response as the trials progressed. Our results suggest that proportional cerebellum size does not necessarily predict an individual's fear response, but rather the habituation process to a fearful stimulus. Cerebellum neuronal density did not predict fear behavior in the individuals which suggests that these effects do not result from changes in neuronal density but due to other variables linked to proportional cerebellum size which might underlie fear habituation.

Keywords
behavioral predictability, domestication, emergence test, isotropic fractionation, neural density
National Category
Behavioral Sciences Biology
Identifiers
urn:nbn:se:du-39866 (URN)10.3389/fphys.2022.826178 (DOI)000765066500001 ()35250629 (PubMedID)2-s2.0-85125852826 (Scopus ID)
Funder
Swedish Research Council Formas, 2019-01508EU, European Research Council, FERALGEN 772874Swedish Research CouncilCarl Tryggers foundation Linköpings universitet
Available from: 2022-03-16 Created: 2022-03-16 Last updated: 2024-01-17Bibliographically approved
Anglart, D., Emanuelson, U., Rönnegård, L. & Sandgren, C. H. (2021). Detecting and predicting changes in milk homogeneity using data from automatic milking systems.. Journal of Dairy Science, 104(10), 11009-11017
Open this publication in new window or tab >>Detecting and predicting changes in milk homogeneity using data from automatic milking systems.
2021 (English)In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 104, no 10, p. 11009-11017Article in journal (Refereed) Published
Abstract [en]

To ensure milk quality and detect cows with signs of mastitis, visual inspection of milk by prestripping quarters before milking is recommended in many countries. An objective method to find milk changed in homogeneity (i.e., with clots) is to use commercially available inline filters to inspect the milk. Due to the required manual labor, this method is not applicable in automatic milking systems (AMS). We investigated the possibility of detecting and predicting changes in milk homogeneity using data generated by AMS. In total, 21,335 quarter-level milk inspections were performed on 5,424 milkings of 624 unique cows on 4 farms by applying visual inspection of inline filters that assembled clots from the separate quarters during milking. Images of the filters with clots were scored for density, resulting in 892 observations with signs of clots for analysis (77% traces or mild cases, 15% moderate cases, and 8% heavy cases). The quarter density scores were combined into 1 score indicating the presence of clots during a single cow milking and into 2 scores summarizing the density scores in cow milkings during a 30-h sampling period. Data generated from the AMS, such as milk yield, milk flow, conductivity, and online somatic cell counts, were used as input to 4 multilayer perceptron models to detect or predict single milkings with clots and to detect milking periods with clots. All models resulted in high specificity (98-100%), showing that the models correctly classified cow milkings or cow milking periods with no clots observed. The ability to successfully classify cow milkings or cow periods with observed clots had a low sensitivity. The highest sensitivity (26%) was obtained by the model that detected clots in a single milking. The prevalence of clots in the data was low (2.4%), which was reflected in the results. The positive predictive value depends on the prevalence and was relatively high, with the highest positive predictive value (72%) reached in the model that detected clots during the 30-h sampling periods. The misclassification rate for cow milkings that included higher-density scores was lower, indicating that the models that detected or predicted clots in a single milking could better distinguish the heavier cases of clots. Using data from AMS to detect and predict changes in milk homogeneity seems to be possible, although the prediction performance for the definitions of clots used in this study was poor.

Keywords
clinical mastitis, clot, dairy cow, multilayer perceptron
National Category
Animal and Dairy Science
Identifiers
urn:nbn:se:du-37830 (URN)10.3168/jds.2021-20517 (DOI)000736976500020 ()34218914 (PubMedID)2-s2.0-85109047518 (Scopus ID)
Available from: 2021-08-04 Created: 2021-08-04 Last updated: 2023-04-14Bibliographically approved
Hallén Sandgren, C., Anglart, D., Klaas, I. C., Rönnegård, L. & Emanuelson, U. (2021). Homogeneity density scores of quarter milk in automatic milking systems.. Journal of Dairy Science, 104(9), 10121-10130
Open this publication in new window or tab >>Homogeneity density scores of quarter milk in automatic milking systems.
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2021 (English)In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 104, no 9, p. 10121-10130Article in journal (Refereed) Published
Abstract [en]

Milk quality and clinical mastitis in dairy cows are monitored by detecting visually abnormal milk. A standardized method to evaluate clots in milk and studies of the incidence and dynamics of clots in milk at the quarter level are lacking. We validated a method to score clot density in quarter milk samples and describe the prevalence and dynamics of the density scores between consecutive samplings and periods in 4 farms with automatic milking systems. Using in-line filters, we collected quarter milk samples at each milking during 3 periods of 30 h each in each farm. Clot density was scored based on coverage of the filter area as 0 (negative), 1 (trace), 2 (mild), 3 (moderate), 4 (heavy), and 5 (very heavy). The score for a specific quarter and milking is referred to as the quarter milking score (QMS). Three assessors independently scored 902 images of filter samples with a Fleiss kappa value of 0.72. In total, 21,202 quarter milk samples from 5,398 milkings of 621 cows were collected. Of the quarter filter samples, 2.4% had visible clots, distributed as mild (1.4%), moderate (0.6%), heavy (0.3%), and very heavy (<0.1%, n = 8). Cases with a cow period sum of QMS ≥ 4, corresponding to 9.4% of all periods, harbored 86% and 94% of all QMS of 2 to 5 and 3 to 5, respectively. Of these cases, cows sampled in all 3 periods and clots in only 1 period had a quarter period sum score ≥ 1 in 1.8 different quarters in average. Corresponding numbers for the cows with clots or traces in 2 or 3 periods were 2.2 and 2.5 different quarters, respectively. A QMS of 2 to 5 in the preceding milking increased the chance of a QMS >1 in the following milking, with an average chance of 38%. The probability of a QMS > 1 increased with increasing previous QMS, a higher sum of QMS during the milking period, longer milking interval, and higher lactation number, but decreased with increasing days in milk. Our study showed that the method of clot-density scoring is feasible to perform and reproducible for investigating the occurrence and dynamics of clots in milk. Elevated clot-density scores clustered within certain cows and cow periods and appeared in new quarters of the cows over time. The low recurrence of QMS of 1 and 2 within quarters indicated that QMS 3 could be a reasonable threshold for detecting quarters with abnormal milk that require further attention.

Keywords
clot, dairy cow, mastitis, quarter milk, score
National Category
Animal and Dairy Science Probability Theory and Statistics
Identifiers
urn:nbn:se:du-37815 (URN)10.3168/jds.2021-20439 (DOI)000687965500038 ()34127261 (PubMedID)2-s2.0-85107826327 (Scopus ID)
Available from: 2021-08-03 Created: 2021-08-03 Last updated: 2023-04-14Bibliographically approved
Patxot, M., Banos, D. T., Kousathanas, A., Orliac, E. J., Ojavee, S. E., Moser, G., . . . Robinson, M. R. (2021). Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications, 12(1), Article ID 6972.
Open this publication in new window or tab >>Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits
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2021 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 6972Article in journal (Refereed) Published
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:du-39016 (URN)10.1038/s41467-021-27258-9 (DOI)000724450600023 ()34848700 (PubMedID)2-s2.0-85120181229 (Scopus ID)
Available from: 2021-12-16 Created: 2021-12-16 Last updated: 2023-04-14Bibliographically approved
Ren, K., Nielsen, P. P., Alam, M. & Rönnegård, L. (2021). Where do we find missing data in a commercial real-time location system? Evidence from 2 dairy farms. JDS Communications, 2, 345-350
Open this publication in new window or tab >>Where do we find missing data in a commercial real-time location system? Evidence from 2 dairy farms
2021 (English)In: JDS Communications, ISSN 2666-9102, Vol. 2, p. 345-350Article in journal (Refereed) Published
Abstract [en]

Real-time indoor positioning using ultra-wideband devices provides an opportunity for modern dairy farms to monitor the behavior of individual cows; however, missing data from these devices hinders reliable continuous monitoring and analysis of animal movement and social behavior. The objective of this study was to examine the data quality, in terms of missing data, in one commercially available ultra-wideband–based real-time location system for dairy cows. The focus was on detecting major obstacles, or sections, inside open freestall barns that resulted in increased levels of missing data. The study was conducted on 2 dairy farms with an existing commercial real-time location system. Position data were recorded for 6 full days from 69 cows on farm 1 and from 59 cows on farm 2. These data were used in subsequent analyses to determine the locations within the dairy barns where position data were missing for individual cows. The proportions of missing data were found to be evenly distributed within the 2 barns after fitting a linear mixed model with spatial smoothing to logit-transformed proportions (mean = 18% vs. 4% missing data for farm 1 and farm 2, respectively), with the exception of larger proportions of missing data along one of the walls on both farms. On farm 1, the variation between individual tags was large (range: 9–49%) compared with farm 2 (range: 12–38%). This greater individual variation of proportions of missing data indicates a potential problem with the individual tag, such as a battery malfunction or tag placement issue. Further research is needed to guide researchers in identifying problems relating to data capture problems in real-time monitoring systems on dairy farms. This is especially important when undertaking detailed analyses of animal movement and social interactions between animals.

National Category
Agricultural and Veterinary sciences Computer and Information Sciences
Research subject
Complex Systems – Microdata Analysis, General Microdata Analysis - methods
Identifiers
urn:nbn:se:du-39055 (URN)10.3168/jdsc.2020-0064 (DOI)
Projects
CSI-DT (SLU)
Funder
Swedish Research Council Formas, 2019-02111
Available from: 2021-12-15 Created: 2021-12-15 Last updated: 2023-04-14Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-1057-5401

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