Mendelian breeding units versus standard sampling strategies: Mitochondrial DNA variation in southwest Sardinia

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits

Genetic diversity of North American captive-born gorillas (Gorilla gorilla gorilla)

Western lowland gorillas (Gorilla gorilla gorilla) are designated as critically endangered and wild populations are dramatically declining as a result of habitat destruction, fragmentation, diseases (e.g., Ebola) and the illegal bushmeat trade. As wild populations continue to decline, the genetic management of the North American captive western lowland gorilla population will be an important component of the long‐term conservation of the species. We genotyped 26 individuals from the North American captive gorilla collection at 11 autosomal microsatellite loci in order to compare levels of genetic diversity to wild populations, investigate genetic signatures of a population bottleneck and identify the genetic structure of the captive‐born population. Captive gorillas had significantly higher levels of allelic diversity (t7 = 4.49, P = 0.002) and heterozygosity (t7 = 4.15, P = 0.004) than comparative wild populations, yet the population has lost significant allelic diversity while in captivity when compared to founders (t7 = 2.44, P = 0.04). Analyses suggested no genetic evidence for a population bottleneck of the captive population. Genetic structure results supported the management of North American captive gorillas as a single population. Our results highlight the utility of genetic management approaches for endangered nonhuman primate species

Genetic Analysis of Putative Familial Relationships in a Captive Chimpanzee (\u3ci\u3ePan troglodytes\u3c/i\u3e) Population

Twelve autosomal dinucleotide repeat loci were analyzed in chimpanzees genomes by DNA amplification using primers designed for analysis of human loci. The markers span the entire length of human chromosomes 21 and 22. Nine markers were polymorphic in chimpanzee as well, with a somewhat comparable level of polymorphism and allele size range. Even in the presence of very limited information and in spite of missing samples, it was possible to reconstruct a complex pedigree and to provide molecular data that corroborate family relationships that were deduced from cage history and behavioral data. The conclusions were further supported by mitochondrial DNA analysis. The data presented in this report show that the extremely abundant source of human markers may be exploited to validate, with molecular evidence, hypotheses on individual relationship or alleged pedigrees, based upon behavioral observations

Integrating Geographic Information into the Analysis of the Genetic Distribution of South African Vervet Monkeys

This project uses the program Geneland to reanalyze McAuliffe’s (2008) thesis data on genetic variability in three South African vervet monkey populations (Polokwane, Oribi and Blyde). Using information on the geographic location and genetic variability of these populations, the spatially explicit Geneland program shows that the three populations are weakly differentiated. These findings oppose the results of previous genetic studies of South African vervet monkeys as well as the results obtained by McAuliffe with the spatially implicit Structure program, which found that the 34 individuals all come from one population. Based on this historic data and the fact that other studies have found the same number of subpopulations with both Structure and Geneland, I conclude that Polokwane, Oribi and Blyde are slightly differentiated, though not distinct enough to be considered separate populations (Latch et al. 2008). These results need to be supported by an analysis of the entire sample of South African vervet monkey genetic data from up to 200 animals prior to suggesting policy changes regarding genetic structuring in South African vervet monkeys

SCREENING OF THE ACID MEAT CONDITION IN THE RENDEMENT NAPOLE GENE USING POLYMERASE CHAIN REACTION - RESTRICTION FRAGMENT LENGTH POLYMORPHISM

A mutation in the rendement napole (RN) gene causes the acid meat condition which results to poor meat quality due to its reduced water holding capacity, low pH, pale color, reduced processing and cooking yield due to increased drip, and strong metallic taste. This study was conducted to detect the mutation in the RN gene in 535 commercial breeder pigs from the Philippines. Blood collection was done then subjected to DNA extraction and genotyping using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) using the enzyme BsrBI, then validated by DNA sequencing. Results revealed that 97.01% of the breeder pigs did not have the mutation in their RN gene, while 2.69% had at least one copy of the defective allele in their gene. The acid meat condition has only been previously detected in the Hampshire breed whereas this study found the mutations predominantly in Pietrain and Landrace breed they were classified as normal (rn/rn), heterozygous mutants (RN/rn), and homozygous mutants (RN/RN) which allowed breeding systems to be developed ensuring that all offspring are free of the defect.  This genetic screening will help in detecting the presence of the defect in a given swine population and reduce the unwanted effects on meat quality thus increasing its market value

Poisson-Furstenberg boundary and growth of groups

We study the Poisson-Furstenberg boundary of random walks on permutational wreath products. We give a sufficient condition for a group to admit a symmetric measure of finite first moment with non-trivial boundary, and show that this criterion is useful to establish exponential word growth of groups. We construct groups of exponential growth such that all finitely supported (not necessarily symmetric, possibly degenerate) random walks on these groups have trivial boundary. This gives a negative answer to a question of Kaimanovich and Vershik.Comment: 24 page

Mendelian breeding units <i>versus</i> standard sampling strategies: mitochondrial DNA variation in southwest Sardinia

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits

UK Housing Market: Time Series Processes with Independent and Identically Distributed Residuals

The paper examines whether a univariate data generating process can be identified which explains the data by having residuals that are independent and identically distributed, as verified by the BDS test. The stationary first differenced natural log quarterly house price index is regressed, initially with a constant variance and then with a conditional variance. The only regression function that produces independent and identically distributed standardised residuals is a mean process based on a pure random walk format with Exponential GARCH in mean for the conditional variance. There is an indication of an asymmetric volatility feedback effect but higher frequency data is required to confirm this. There could be scope for forecasting the index but this is tempered by the reduction in the power of the BDS test if there is a non-linear conditional variance process

Cross Species use of Human Microarray Genotyping Technology for Bornean Orangutan (Pongo pygmaeus) SNP Discovery

Previous genetic studies of orangutans (Pongo spp.) have relied mainly upon mitochondrial DNA or microsatellite short tandem repeats (STR) for genomic genotyping analysis. Scientists have yet to take advantage of the genetic closeness of the great apes to humans for genomic analysis by using advanced techniques available for human genotyping. To genotype orangutans at Tanjung Puting National Park, we developed a novel combination of a methyl-based magnetic enrichment capture of genomic fecal DNA with genotyping on a human targeted single nucleotide polymorphism (SNP) microarray, and compared this to additional microsatellite (STR) micro-capillary genotyping. We successfully isolated 125 known human genomic SNP loci (0.08% of those targeted) which hybridized orangutan DNA on the human targeted Illumina Infinium QC array. We estimated genetic diversity and relatedness (r) using three estimators for a total of 32 (21 female and 9 male) wild orangutans at the Camp Leakey study site. Average TrioML relatedness within the sample, estimated from our combo SNP/STR dataset, was at a range consistent with half and first cousins (r = .082). All sampled males and females had relatives within the study site indicating we have verified a local, closely related community of wild orangutans at Camp Leakey