INFERRING PURGING FROM PEDIGREE DATA

@inproceedings{Gulisija2007INFERRINGPF,
  title={INFERRING PURGING FROM PEDIGREE DATA},
  author={Davorka Gulisija and James F. Crow},
  booktitle={Evolution; international journal of organic evolution},
  year={2007}
}
Abstract The harmful effects of inbreeding can be reduced if deleterious recessive alleles were removed (purged) by selection against homozygotes in earlier generations. If only a few generations are involved, purging is due almost entirely to recessive alleles that reduce fitness to near zero. In this case the amount of purging and allele frequency change can be inferred approximately from pedigree data alone and are independent of the allele frequency. We examined pedigrees of 59,778 U.S… 
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  • J. Cole
  • Medicine, Biology
    Genetics Selection Evolution
  • 2015
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References

SHOWING 1-10 OF 20 REFERENCES
AN ESTIMATE OF THE MUTATIONAL DAMAGE IN MAN FROM DATA ON CONSANGUINEOUS MARRIAGES.
TLDR
Calculations are presented whereby, using death rates both from Arner's and from two other published studies of consanguineous marriages, the total mutational damage is attempted to measure, by making some assumptions about the manner in which the mutations are expressed, the amount of mutationaldamage actually expressed each generation.
Ancestral inbreeding only minimally affects inbreeding depression in mammalian populations.
TLDR
Results show a small but highly significant trend of purging on neonatal survival, and two different regression models (an ancestral inbreeding model and a lethal recessive model) are used to test for the presence of purge effects in 25 captive mammalian populations.
Do Plant Populations Purge Their Genetic Load? Effects of Population Size and Mating History on Inbreeding Depression
TLDR
Regression analyses suggest that purging is most likely to ameliorate ID for early traits, but these declines are typically modest (5–10%).
The influence of epistasis on homozygous viability depression in Drosophila melanogaster.
TLDR
The results to be presented here show no statistically significant systematic interaction between mildly deleterious homozygotes on the two major autosomes, indicating that within a chromosome there is a barely significant synergistic interaction.
A Comparison of the Effect of Lethal and Detrimental Chromosomes from Drosophila Populations.
HIS study was undertaken in an attempt to determine whether the effects of recurrent mutation on the population and the deleterious effects of inbreeding are due primarily to a small number of genes
Reduced genetic load revealed by slow inbreeding in Drosophila melanogaster.
TLDR
It can be concluded that homozygous genotypes from which deleterious genes of major effect have been eliminated during slow inbreeding may show far less depression in reproductive fitness than suggested by earlier studies of wild chromosome homozygotes.
Homozygous viability and fertility loads in Drosophila melanogaster.
TLDR
Interest centers upon the relative impact of the group of genes with individually slight effects in contrast to those with drastic effects, and an additional aspect of fitness, that of female and male fertility, has also been investigated.
Effect of selection against deleterious mutations on the decline in heterozygosity at neutral loci in closely inbreeding populations.
TLDR
Transition matrices for selfing and full-sib mating were derived to investigate the effect of selection against deleterious mutations on the process of inbreeding at a linked neutral locus, and stochastic simulations results are in general compatible with empirical observations.
Coefficients of Inbreeding and Relationship
TLDR
The importance of having a coefficient by means of which the degree of inbreeding may be expressed has been brought out by Pearl' in a number of papers published between 1913 and 1917.
Introduction to quantitative genetics
TLDR
For the next few weeks the course is going to be exploring a field that’s actually older than classical population genetics, although the approach it’ll be taking to it involves the use of population genetic machinery.
...
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