Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Sanna D

PROVIDER: S-EPMC3115307 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Sanna Daria D Pala Maria M Cossu Piero P Dedola Gian Luca GL Melis Sonia S Fresu Giovanni G Morelli Laura L Obinu Domenica D Tonolo Giancarlo G Secchi Giannina G Triunfo Riccardo R Lorenz Joseph G JG Scheinfeldt Laura L Torroni Antonio A Robledo Renato R Francalacci Paolo P

Genetics and molecular biology 20110401 2

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 ...[more]

PMID: 21734814

Similar Datasets

Project description:Sampling approaches used to census and monitor populations of flora and fauna are diverse, ranging from simple random sampling to complex hierarchal stratified designs. Usually the approach taken is determined by the spatial and temporal distribution of the study population, along with other characteristics of the focal species. Long-term monitoring programs used to assess seabird population trends are facilitated by their high site fidelity, but are often hampered by large and difficult to access colonies, with highly variable densities that require intensive survey. We aimed to determine the sampling effort required to (a) estimate population size with a high degree of confidence, and (b) detect different scenarios of population change in a regionally important species in the Atlantic, the Manx shearwater (Puffinus puffinus). Analyses were carried out using data collected from tape-playback surveys on four islands in the North Atlantic. To explore how sampling effort influenced confidence around abundance estimates, we used the heuristic approach of imagining the areas sampled represented the total population, and bootstrapped varying proportions of subsamples. This revealed that abundance estimates vary dramatically when less than half of all plots (n dependent on the size of the site) is randomly subsampled, leading to an unacceptable lack of confidence in population estimates. Confidence is substantially improved using a multi-stage stratified approach based on previous information on distribution in the colonies. In reality, this could lead to reducing the number of plots required by up to 80%. Furthermore, power analyses suggested that random selection of monitoring plots using a matched pairs approach generates little power to detect overall population changes of 10%, and density-dependent changes as large as 50%, because variation in density between plots is so high. Current monitoring programs have a high probability of failing to detect population-level changes due to inappropriate sampling efforts. Focusing sampling in areas of high density with low plot to plot variance dramatically increases the power to detect year to year population change, albeit at the risk of not detecting increases in low density areas, which may be an unavoidable strategy when resources are limited. We discuss how challenging populations with similar features to seabirds might be censused and monitored most effectively.

Project description:BackgroundIn species with biparental care both members of the breeding pair cooperate to raise the offspring either by assisting each other in every reproductive task or by specializing in different ones. The latter case is known as reproductive role specialization. Raptors are considered one of the most role-specialized groups, but little is known about parental behavior away from the nest. Until the advent of biologgers, avian role specialization was traditionally studied with direct observations at the nest because of the difficulties of following and recording the behavior of free-ranging individuals. In this paper we analyze how the role specialization of the lesser kestrel (Falco naumanni) influences foraging movement patterns throughout the breeding season. We tracked 30 lesser kestrel breeders from two breeding colonies using high-frequency GPS-dataloggers during four consecutive breeding seasons.ResultsWe found no differences between sexes in lesser kestrel foraging movements early in the breeding season before the formation of the breeding pair. However, we observed sexually distinct foraging movement strategies later in the breeding season once breeding pairs were formed. Lesser kestrel males performed a large number of short foraging trips while females made a few long ones. This maximized the provisioning rate by males to feed their mates and offspring. Meanwhile, lesser kestrel females spent more time at the colony than males in order to defend the nest, incubate the eggs and brood the nestlings. Females also helped their mates to provision the nestling once these had grown and required more food and less protection. Furthermore, lesser kestrels showed a sexual spatial segregation in foraging areas, with males foraging closer to the colony than females.ConclusionsThe lesser kestrel responds to changes in energy demand throughout the breeding season with its foraging movement strategy, but in a different way depending on parental sex. The sexual spatial segregation observed is likely to be the result of an adaptive foraging strategy based on role specialization to reduce prey depletion close to the colony and intersexual competition in order to improve breeding success.

Project description:Parkinson's disease is a common, progressive neurodegenerative disorder, affecting 3% of those older than 75 years of age. Clinically, Parkinson's disease (PD) is associated with resting tremor, postural instability, rigidity, bradykinesia, and a good response to levodopa therapy. Over the last 15 years, numerous studies have confirmed that genetic factors contribute to the complex pathogenesis of PD. Highly penetrant mutations producing rare, monogenic forms of the disease have been discovered in singular genes such as SNCA, Parkin, DJ-1, PINK 1, LRRK2, and VPS35. Unique variants with incomplete penetrance in LRRK2 and GBA have been shown to be strong risk factors for PD in certain populations. Additionally, over 20 common variants with small effect sizes are now recognized to modulate the risk for PD. Investigating Mendelian forms of PD has provided precious insight into the pathophysiology that underlies the more common idiopathic form of disease; however, no treatment methodologies have developed. Furthermore, for identified common risk alleles, the functional basis underlying risk principally remains unknown. The challenge over the next decade will be to strengthen the findings delivered through genetic discovery by assessing the direct, biological consequences of risk variants in tandem with additional high-content, integrated datasets. This review discusses monogenic risk factors and mechanisms of Mendelian inheritance of Parkinson disease. Highly penetrant mutations in SNCA, Parkin, DJ-1, PINK 1, LRRK2 and VPS35 produce rare, monogenic forms of the disease, while unique variants within LRRK2 and GBA show incomplete penetrance and are strong risk factors for PD. Additionally, over 20 common variants with small effect sizes modulate disease risk. The challenge over the next decade is to strengthen genetic findings by assessing direct, biological consequences of risk variants in tandem with high-content, integrated datasets. This article is part of a special issue on Parkinson disease.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets