85 research outputs found

    How To Perform Meaningful Estimates of Genetic Effects

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    Although the genotype-phenotype map plays a central role both in Quantitative and Evolutionary Genetics, the formalization of a completely general and satisfactory model of genetic effects, particularly accounting for epistasis, remains a theoretical challenge. Here, we use a two-locus genetic system in simulated populations with epistasis to show the convenience of using a recently developed model, NOIA, to perform estimates of genetic effects and the decomposition of the genetic variance that are orthogonal even under deviations from the Hardy-Weinberg proportions. We develop the theory for how to use this model in interval mapping of quantitative trait loci using Halley-Knott regressions, and we analyze a real data set to illustrate the advantage of using this approach in practice. In this example, we show that departures from the Hardy-Weinberg proportions that are expected by sampling alone substantially alter the orthogonal estimates of genetic effects when other statistical models, like F2 or G2A, are used instead of NOIA. Finally, for the first time from real data, we provide estimates of functional genetic effects as sets of effects of natural allele substitutions in a particular genotype, which enriches the debate on the interpretation of genetic effects as implemented both in functional and in statistical models. We also discuss further implementations leading to a completely general genotype-phenotype map

    Conservation implications of the mating system of the Pampa Hermosa landrace of peach palm analyzed with microsatellite markers

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    Peach palm (Bactris gasipaes) is cultivated by many indigenous and traditional communities from Amazonia to Central America for its edible fruits, and is currently important for its heart-of-palm. The objective of this study was to investigate the mating system of peach palm, as this is important for conservation and breeding. Eight microsatellite loci were used to genotype 24 open-pollinated progenies from three populations of the Pampa Hermosa landrace maintained in a progeny trial for genetic improvement. Both the multi-locus outcrossing rates (0.95 to 0.99) and the progeny level multi-locus outcrossing rates (0.9 to 1.0) were high, indicating that peach palm is predominantly allogamous. The outcrossing rates among relatives were significantly different from zero (0.101 to 0.202), providing evidence for considerable biparental inbreeding within populations, probably due to farmers planting seeds of a small number of open-pollinated progenies in the same plot. The correlations of paternity estimates were low (0.051 to 0.112), suggesting a large number of pollen sources (9 to 20) participating in pollination of individual fruit bunches. Effective population size estimates suggest that current germplasm collections are insufficient for long-term ex situ conservation. As with most underutilized crops, on farm conservation is the most important component of an integrated conservation strategy

    High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model

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    Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate) to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS), were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50%) of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284) and intronic regions (169) with the least in exon\u27s (4), suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a), excitatory receptors (Grin2a, Gria3, Grip1), neurotransmitters (Pomc), and synapses (Snap29). This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits

    Improving community health networks for people with severe mental illness : a case study investigation

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    Introduction Policy drivers in mental health to address personal recovery, stigma and poor physical health indicate that new service solutions are required. This study aimed to understand how connections to people, places and activities were utilised by individuals with severe mental illness (SMI) to benefit health and wellbeing. Methods A five-module mixed-methods design was undertaken in two study sites. Data were collected from 150 network-mapping interviews and 41 in-depth follow-up interviews with people with SMI; in-depth interviews with 30 organisation stakeholders and 12 organisation leaders; and 44 telephone interviews with practitioners. We undertook a three-stage synthesis process including independent lived experience feedback, and a patient and public involvement team participated in tool design, data collection, analysis and write-up. Results Three personal network types were found in our study using the community health network approach: diverse and active; family and stable; formal and sparse. Controlled for other factors we found only four variables significantly associated with which network type a participant had: living alone or not; housing status; formal education; long-term sickness or disability. Diagnosis was not a factor. These variables are challenging to address but they do point to potential for network change. The qualitative interviews with people with SMI provided further understanding of connection-building and resource utilisation. We explored individual agency across each network type, and identified recognition of the importance and value of social support and active connection management alongside the risks of isolation, even for those most affected by mental illness. We identified tensions in personal networks, be that relationships with practitioners or families, dealing with the impact of stigma, or frustrations of not being in employment, which all impact on network resources and well-being. The value of connectedness within personal networks of people, place and activity for supporting recovery was evident in shaping identity, providing meaning to life and sense of belonging, gaining access to new resources, structuring routines and helping individuals ‘move on’ in their recovery journey. Health-care practitioners recognised that social factors were important in recovery but reported system-level barriers (workload, administrative bureaucracy, limited contact time with clients) in addressing these issues fully. Even practitioners working in third-sector services whose remit involved increasing clients’ social connection faced restrictions due to being evaluated by outcome criteria that limited holistic recovery-focused practices. Service providers were keen to promote recovery-focused approaches. We found contrasts between recovery ideology within mental health policy and recovery practice on the ground. In particular, the social aspects of supporting people with SMI are often underprioritised in the health-care system. In a demanding and changing context, strategic multiagency working was seen as crucial but we found few examples of embedded multisector organisation partnerships. Conclusion While our exploratory study has limitations, findings suggest potential for people with SMI to be supported to become more active managers of their personal networks to support well-being regardless of current network type. The health and social care system does not currently deliver multiagency integrated solutions to support SMI and social recovery

    Microsatellite DNA variation indicates low levels of genetic differentiation among cuttlefish (Sepia officinalis L.) populations in the English Channel and the Bay of Biscay

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    Population substructure of the cuttlefish Sepia officinalis (Mollusca: Cephalopoda), as investigated by genetic variation of microsatellite loci, has been reported to be significantly extensive around the Iberian Peninsula with FST = 0.061 (Pérez-Losada et al. 2002) and panmictic in the semi-enclosed Adriatic Sea with FST = 0.011 (Garoia et al. 2004). Yet, no verified genetic information on population substructure existed for the northern distribution range of this species in the English Channel and Bay of Biscay.So far, reproductive and migration behaviour and in-vitro oxygen binding properties of haemocyanin have suggested existence of separate populations in the English Channel and the Bay of Biscay. Examination of genetic variation at seven microsatellite loci within samples from the Bay of Biscay, the English Channel and the southern North Sea indicated low levels of genetic differentiation in this area but also a breakdown of free gene flow at highly significant average FST = 0.018. Although there is a considerable genetic exchange between populations of S. officinalis in the English Channel and the Bay of Biscay, they cannot be regarded as a single, freely interbreeding population. Earlier reported biological differences might thus be due to genetic variability between the populations
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