Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Cryptosporidium spp. in ruminants at the Lisbon Zoo.

Feces from 34 species of ruminants housed at the Lisbon Zoo was examined for Cryptosporidium spp. oocysts. Three hundred and eighty-eight samples were analyzed. Three hundred and eighty species-specific group fecal samples were collected monthly, from September 1998 until August 1999, along with eight individual specimens from eight neonates. All samples were examined by four different techniques: microscopic observation of direct and concentrated fecal smears, staining with modified Ziehl-Nielsen, immunofluorescent assay, and immunoenzymatic assay. The prevalence of infection was 3.6%. Five neonates with diarrhea were infected. Cryptosporidial oocysts were shed more frequently during winter months. Some facilities may have permitted oocysts to remain viable, possibly contributing to cryptosporidial transmission between animals.     

Dual mycotic infection in a chicken

A double mycotic infection, caused by Aspergillus fumigatus and a zygomycete-like organism, was histopathologically demonstrated in the lungs of a 12-week-old chicken. A. fumigatus was isolated, but the zygomycete was not.     

Fragmentation patterns of the Caatinga drylands

Context

Biodiversity is modulated by the spatial structure of the landscape. Thus, landscape metrics can be useful indicators of biota integrity and vulnerability, helping in conservation and management decisions.

Objective

We performed the first quantitative analysis of the spatial structure of the Caatinga drylands. We estimated the habitat amount and the fragmentation pattern of this region using a multi-scale perspective.

Methods

Using the Brazilian official database of native remnants, we calculated the number and percentage of remaining fragments per size class and we describe how habitat amount changes along the landscape. By simulating different dispersal capacities, we estimated the functional connectivity among remnants. We also calculated the cumulative core area as a function of different edge effect widths.

Results

Caatinga is subdivided into 47,100 fragments. Although 91% of them are smaller than 500 ha, 720 fragments are larger than 10,000 ha, corresponding to 78% of the remaining vegetation. Potentially, 95% of the vegetation is accessible to species that can cross 1000 m of matrix. With one kilometer of edge effect, the core area is reduced to a quarter of the remaining vegetation. The habitat amount analyzes reinforced the regional differences in the spatial distribution of the remnants.

Conclusions

Caatinga remains well connected for species with moderate and high dispersal capacities. However much of its remaining area is vulnerable to anthropogenic disturbances. Expansion of the protected area network and effective natural resource management to avoid overexploitation of the remnants are key strategies for maintaining the Caatinga biodiversity and its services.

     

Nutritional planning for Nellore heifers post-weaning to conception at 15 months of age: performance and nutritional,metabolic, and reproductive responses

Tropical Animal Health and Production - The objective of this study was to evaluate the effects of strategic supplementation in the dry period and dry/rainy transition period on the performance and...     

Early luteal development in Santa Inês ewes superovulated with reduced doses of porcine follicle‐stimulating hormone

The aim was to compare the early luteal development in ewes superovulated with different doses of pFSH. Twenty‐nine Santa Inês ewes received a progesterone device (CIDR®) for 8 days. Gonadotrophic treatment started on Day 6: G200 (control, n = 9, 200 mg); G133 (n = 10, 133 mg); and G100 (n = 10, 100 mg of pFSH). On Day 6, all females received eCG (300 IU). B‐mode and spectral Doppler ultrasonography were performed daily during the early luteal phase (Days 11–15) to monitor the development of corpora lutea (CLs; dimensions) and ovarian arteries indices. CLs were also classified as normal or prematurely regressed (PRCL) on Day 15 by videolaparoscopy. Ewes from G100 and G133 showed gradual increase in luteal diameter during the early luteal phase (p < 0.001), whereas G200 animals presented increase from Day 11 to Day 13, and then decrease on Days 14 and 15 (p < 0.001). The G200 females showed greater percentage of PRCL (45.20%) than those of the other groups (p < 0.001). The normal CLs number was greater in G100 than in G133 (p = 0.04), while the PRCL number was greater in G200 than in the other groups (p = 0.03). Resistive index (RI) was greater in G200 than in G100 (p = 0.02). RI was lower in Day 12 than Day 15 (p = 0.02). Pulsatility index (PI) was greater on Days 14 and 15 (p < 0.01). In conclusion, the lowest dose of pFSH (100 mg) can be considered sufficient for an efficient superovulatory response in sheep, producing better CLs development dynamic in early luteal phase and ovarian blood perfusion and smaller number of PRCL than the traditional (200 mg) pFSH dose.     

Combined treatment with oestradiol benzoate,d‐cloprostenol and oxytocin permits cervical dilation and nonsurgical embryo recovery in ewes

This study examined the feasibility of transcervical embryo recovery after the hormonal treatment to induce cervical dilation, following the 7‐day oestrous synchronization protocol in multiparous Santa Inês ewes. A total of 23 cyclic ewes received two doses of 37.5 μg of d‐cloprostenol by latero‐vulvar route 7 days apart. After the second injection of d‐cloprostenol, the ewes were checked for oestrus (every 12 hr) and then mated by fertile rams throughout the oestrous period. All ewes received 37.5 μg of d‐cloprostenol (latero‐vulvar) and 1 mg of oestradiol benzoate by either intramuscular (EBim group; n = 12) or intravaginal (EBivg group; n = 11) route 16 hr before embryo flushing. Twenty minutes before the flushing, 50 IU of oxytocin were administered intravenously. The oestrous response (i.e., the percentage of ewes that showed signs of oestrous behaviour after the second d‐cloprostenol injection) was 91.3% (21/23). The proportion of successfully penetrated ewes (81.8% compared with 80.0%), the mean duration of embryo flushing (24.7 ± 2.0 min compared 26.2 ± 1.9 min), the flushing fluid recovery rate (94.8 ± 1.3% compared with 91.0 ± 2.9%) and the average number of structures recovered per ewe (0.5 ± 0.4 compared with 0.8 ± 0.4) did not vary (p > 0.05) between the EBim and EBivg groups. Viable embryos were recovered from 41.2% (7/17) of successfully penetrated ewes. It can be concluded that nonsurgical (i.e., transcervical) embryo collection can be performed in oestrous‐synchronized Santa Inês ewes pretreated with d‐cloprostenol, oxytocin and oestradiol benzoate, with the latter hormone administered by either the intramuscular or intravaginal route.