D. Vankan

Bull selection and use in northern Australia 4. Calf output and predictors of fertility of bulls in multiple-sire herds

On 10 northern Australian properties, the number of calves sired (calf output) by individual bulls in multiple-sire matings was measured by DNA typing for paternity. There were 235 bulls (92 Santa Gertrudis, 25 5/8 Brahman and 119 Brahman) from 37 multiple-sire mating groups. Number of bulls in groups ranged from 2 to 25 and ages of bulls ranged from 2 to 5 years. Mating periods were for 3-12 months and bull mating percentages were 2.5-6%. In all, there were 4251 calves tested and the resolution of paternity ranged from 92.5 to 100% and averaged 97.7% across all sites. This included 9.9% of calves with no potential sires in any of the mating groups. Of the 235 bulls mated, 58% sired 10% or less calves in each of their respective mating groups with 6% not siring any calves. In contrast, 14% sired over 30% of the calves in each of the respective mating groups. When bulls were mated in groups of 8-24, the maximum percent of calves sired by individual bulls was 26+/-7% (mean+/-S.D.) with a range 11-36%. However, when bulls were mated in groups of 2-7, the maximum percent of calves sired by individual bulls was 59+/-19% with a range 24-94%. Calf output of bulls was moderately repeatable across years at four of five sites. Multiple regression models relating pre-mating measures of physical, seminal and behavioural traits to calf output were developed for the three breed groups. In all, only 138 of the 235 bulls were included in the models (40 Santa Gertrudis, 24 5/8 Brahman and 74 Brahman). Sheath and testicular traits, such as scrotal circumference and testicular tone, were generally not related to calf output, the exceptions being sheath depth in Brahman bulls which was negatively related (P<0.05) and scrotal circumference in 5/8 Brahmans which was positively related (P=0.08) to calf output. Dominance was only included in the 5/8 Brahman model but there was no significant relationship between dominance hierarchy and calf output. Semen motility was only related (P<0.05) to calf output in 5/8 Brahmans. However, measures of semen quality based on spermatozoa morphology were important contributors to calf output in the Santa Gertrudis and Brahman models where percent normal spermatozoa was positively related (P<0.01) to calf output. In Santa Gertrudis and Brahman bulls, measures of sexual behaviour in the serving capacity test were related to calf output. In Santa Gertrudis, these were for the number of displays of sexual interest (P<0.05), and mounts (P<0.01), but not number of serves, whilst in Brahman bulls, libido score was positively related to calf output (P<0.05). The models only explained 35-57% of the variation in calf output.

Phylogenetic and phylogeographic relationships in Ixodes holocyclus and Ixodes cornuatus (Acari: Ixodidae) inferred from COX1 and ITS2 sequences

We inferred the phylogenetic and phylogeographic relationships in ticks, which were identified morphologically as Ixodes holocyclus and Ixodes cornuatus, from mitochondrial cytochrome oxidase subunit 1 (COX1) and nuclear internal transcribed spacer 2 (ITS2) sequences. We obtained COX1 (640bp) and ITS2 (527-568bp) sequences from 429 ticks from 49 localities in Tasmania, Victoria, New South Wales and Queensland, Australia. Our analyses show that there are two species of Ixodes in eastern Australia that cause paralysis in dogs and other mammals: I. holocyclus and I. cornuatus. Further, we conclude that the morphological criteria used to differentiate female I. holocyclus and I. cornuatus are equivocal but I. holocyclus can be distinguished from I. cornuatus using COX1 and/or ITS2 sequences. Intraspecific genetic variation in I. holocyclus and I. cornuatus was less than 0.86% and 0.19% for COX1 and ITS2, respectively. Ixodes holocyclus could be genetically distinguished between different geographic ranges. There were no significant genetic differences between I.cornuatus from Tasmania and mainland Australia, but there are some COX1 haplotypes of I. cornuatus from the mainland that were not detected in Tasmanian and vice versa.

Developmental validation of DogFiler, a novel multiplex for canine DNA profiling in forensic casework

While the analysis of human DNA has been the focus of large-scale collaborative endeavors, non-human forensic DNA analysis has not benefited from the same funding streams and coordination of effort. Consequently, the development of standard marker panels, allelic ladders and allele-specific sequence data comparable to those established for human forensic genetics has lagged. To meet that need for domestic dogs, we investigated sequence data provided by the published 7.6X dog genome for novel short tandem repeat markers that met our criteria for sensitivity, stability, robustness, polymorphic information content, and ease of scoring. Fifteen unlinked tetranucleotide repeat markers were selected from a pool of 3113 candidate markers and assembled with a sex-linked marker into a multiplex capable of generating a full profile with as little as 60pg of nuclear DNA. An accompanying allelic ladder was assembled and sequenced to obtain detailed repeat motif data. Validation was carried out according to SWGDAM guidelines, and the DogFiler panel has been integrated into forensic casework and accepted in courts across the U.S. Applying various formulae for calculating random match probabilities for inbred populations, estimates for this panel of markers have proven to be comparable to those obtained in human forensic genetics. The DogFiler panel and the associated allelic ladder represent the first published non-human profiling system to fully address all SWGDAM recommendations.

Genetic identification of wild Asian water buffalo in Nepal

The wild water buffalo is highly endangered, with the few remaining populations already affected or likely to be increasingly affected by hybridization with domestic buffalo. The work described here was done to evaluate a genetic method to discriminate wild from mixed ancestry (hybrid) and domestic animals, and to identify with high probability those most likely to be purebred wild. Samples from 45 animals (phenotypically classified into three groups - ten wild, 28 domestic and seven hybrid) were genotyped for ten microsatellite loci. Although genetic distances among the three groups were small, an assignment test identified two of the ‘wild’ and seven of the ‘domestic’ as hybrids. However, sample sizes also are small, indicating the need for a conservative approach in the first instance in using these results. As more animals are genotyped, assignments will become more accurate, and a translocation programme to establish a second Nepalese wild population in a protected area could be undertaken.

Cat ownership perception and caretaking explored in an internet survey of people associated with cats

People who feed cats that they do not perceive they own (sometimes called semi-owners) are thought to make a considerable contribution to unwanted cat numbers because the cats they support are generally not sterilized. Understanding people’s perception of cat ownership and the psychology underlying cat semi-ownership could inform approaches to mitigate the negative effects of cat semi-ownership. The primary aims of this study were to investigate cat ownership perception and to examine its association with human-cat interactions and caretaking behaviours. A secondary aim was to evaluate a definition of cat semi-ownership (including an association time of ≥1 month and frequent feeding), revised from a previous definition proposed in the literature to distinguish cat semi-ownership from casual interactions with unowned cats. Cat owners and semi-owners displayed similar types of interactions and caretaking behaviours. Nevertheless, caretaking behaviours were more commonly displayed towards owned cats than semi-owned cats, and semi-owned cats were more likely to have produced kittens (p<0.01). All interactions and caretaking behaviours were more likely to be displayed towards cats in semi-ownership relationships compared to casual interaction relationships. Determinants of cat ownership perception were identified (p<0.05) and included association time, attachment, perceived cat friendliness and health, and feelings about unowned cats, including the acceptability of feeding unowned cats. Encouraging semi-owners to have the cats they care for sterilized may assist in reducing the number of unwanted kittens and could be a valuable alternative to trying to prevent semi-ownership entirely. Highly accessible semi-owner “gatekeepers” could help to deliver education messages and facilitate the provision of cat sterilization services to semi-owners. This research enabled semi-ownership to be distinguished from casual interaction relationships and can assist welfare and government agencies to identify cat semi-owners in order to develop strategies to address this source of unwanted cats.

Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region

The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y‐chromosomal ZFY, SRY and DBY sequences. Swamp buffalo has a higher diversity of both maternal and paternal lineages than river buffalo, with also a remarkable contrast between a weak phylogeographic structure of river buffalo and a strong geographic differentiation of swamp buffalo. The highest diversity of the swamp buffalo maternal lineages was found in south China and north Indochina on both banks of the Mekong River, while the highest diversity in paternal lineages was in the China/Indochina border region. We propose that domestication in this region was later followed by introgressive capture of wild cows west of the Mekong. Migration to the north followed the Yangtze valley as well as a more eastern route, but also involved translocations of both cows and bulls over large distances with a minor influence of river buffaloes in recent decades. Bayesian analyses of various migration models also supported domestication in the China/Indochina border region. Coalescence analysis yielded consistent estimates for the expansion of the major swamp buffalo haplogroups with a credibility interval of 900 to 3900 years BP. The spatial differentiation of mtDNA and Y‐chromosomal haplotype distributions indicates a lack of gene flow between established populations that is unprecedented in livestock.

Cross-Sectional Study of Characteristics of Owners and Nonowners Surrendering Cats to Four Australian Animal Shelters

Unwanted cats surrendered to nonhuman animal shelters are generally categorized as either “owned” or “stray.” This classification is misleading because “stray” cats may include many “semiowned” cats, for which people provide care but who are not perceived as being owned. This differentiation is important because effective strategies designed to reduce cat admissions to, and euthanasia rates in, shelters rely on accurate information about cat populations contributing to shelter intake; cat semiowners will likely respond to different strategies than people with no relationship with the cats they surrender. People surrendering cats to four Australian animal shelters were surveyed to identify factors associated with perception of ownership. Many self-classified nonowners had fed the cats they surrendered, often for a considerable period of time. The factor most strongly associated with ownership perception was an increasing association time with the cat. These findings confirm that enduring relationships between surrenderers and cats, consistent with cat semiownership, are common for cats surrendered to Australian animal shelters. This finding should be taken into account when planning education messages and cat population management strategies aimed at reducing cat admissions.

Real-time PCR genotyping and frequency of the myostatin F94L mutation in beef cattle breeds.

This research developed two real-time PCR assays, employing high-resolution melt and allele-specific analysis to accurately genotype the F94L mutation in cattle. This mutation (g.433C > A) in the growth differentiation factor 8 or myostatin gene has recently been shown to be functionally associated with increased muscle mass and carcass yield in cattle. The F94L mutation is not, like other myostatin mutations, associated with reduced fertility and dystocia. It is therefore a candidate for introgression into other breeds to improve retail beef yield and the development of a simple and accurate test to genotype this specific mutation is warranted. Variations in the efficiency of enzyme cleavage compromised the accuracy of genotyping by published methods, potentially resulting in an overestimation of the frequency of the mutant allele. The frequency of the F94L mutation was determined by real-time PCR in 1140 animals from 15 breeds of cattle in Australia. The mutation was present in Simmental (0.8%), Piedmontese (2%), Droughtmaster (4%) and Limousin (94.2%) but not found in Salers, Angus, Poll Hereford, Hereford, Gelbvieh, Charolais, Jersey, Brahman, Holstein, Shorthorn or Maine Anjou. The low prevalence of F94L in all beef breeds except Limousin indicates the significant potential for this mutation to improve retail yield in Australian beef cattle.

Comparison of metabolic, hematological, and peripheral blood leukocyte cytokine profiles of dairy cows and heifers during the periparturient period.

The periparturient period presents major physiological challenges for the dairy cow. It is a period that is affected by metabolic stressors, major changes in endocrine status, and altered immune function, which together result in an increased risk of disease. Immunological, hematological, and metabolic profiles from the periparturient period of heifers (primipara) were compared with those of cows (pluripara) to test the hypothesis that at the time of calving they have qualitatively different peripheral blood profiles. Blood samples were collected from 22 Holstein-Friesian animals on 3 occasions: approximately 2 wk before calving, within 24h after calving, and approximately 2 wk after calving. Quantitative PCR was used to measure the expression of a selected set of cytokines and receptors by peripheral blood leukocytes. Additional analyses included hemoglobin concentration, red cell, platelet and white cell counts (total and differentiated), and clinical diagnostic biochemical profiles. Total leukocyte counts, neutrophils, and lymphocytes were higher in heifers than cows before calving and within 24h after calving. Alkaline phosphatase was consistently higher in heifers than cows and several significant differences were observed between the 2 groups with regards to cytokine and cytokine-receptor mRNA expression. The results warrant further investigation from the perspective of identifying risk factors for metabolic and parturient disease in dairy cattle.

Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: inferences on the region of domestication of the swamp buffalo.

Data from three published studies of genetic variation at 18 microsatellite loci in water buffalo populations in China (18 swamp type, two river type), Nepal (one wild, one domestic river, one hybrid) and south-east Asia (eight swamp, three river) were combined so as to gain a broader understanding of genetic relationships among the populations and their demographic history. Mean numbers of alleles and expected heterozygosities were significantly different among populations. Estimates of θ (a measure of population differentiation) were significant among the swamp populations for all loci and among the river populations for most loci. Differentiation among the Chinese swamp populations (which was due primarily to just one population) was much less than among the south-east Asian. The Nepal wild animals, phenotypically swamp type but genetically like river type, are significantly different from all the domestic river populations and presumably represent the ancestral Bubalus arnee (possibly with some river-type introgression). Relationships among the swamp populations (D(A) genetic distances, principal component analysis and structure analyses) show the south-east Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo.