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A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.
TLDR
A strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination is presented.
Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum.
TLDR
This paper shows how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that is due to historical events.
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination.
TLDR
An algorithm for defining a nested statistical design under cladogram uncertainty and recombination is presented and it is illustrated that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis.
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila.
TLDR
A cladogram is produced that partially reconstructs the evolutionary history of the present-day haplotype variability in Drosophila melanogaster by producing a nested analysis of variance that simultaneously detects phenotypic effects, localizes the effects within the cladogram, and identifies haplotypes that are potentially heterogeneous in their Phenotypic associations.
Estimates of Lethal Equivalents and the Cost of Inbreeding in Mammals
TLDR
The cost of inbreeding in natural populations of mammals are unknown despite their theoretical importance in genetic and sociobiological models and practical applications in conservation biology, and the regression of juvenile survival on the inbreeding coefficient using pedigrees of 40 captive mammalian populations belonging to 38 species is estimated.
Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction.
TLDR
This work has shown that haplotype frequency in the sample contains information on the topological position of a given haplotype in a cladogram, which will allow one to reduce the number of alternative phylogenies and incorporate the uncertainties involved in reconstructing intraspecific phylogenies into subsequent analyses that depend heavily in the topology of the tree.
Population Genetics And Microevolutionary Theory
TLDR
The scope and basic Premises of Population Genetics are outlined, including basic Quantitative Genetic Definitions and Theory, and the mechanisms of Natural Selection with Other Evolutionary Forces are modeled.
Out of Africa and back again: nested cladistic analysis of human Y chromosome variation.
TLDR
It is inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model.
Using phylogeographic analyses of gene trees to test species status and processes
TLDR
By using gene trees in this manner, species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation.
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping or DNA sequencing. V. Analysis of case/control sampling designs: Alzheimer's disease and
TLDR
This analysis indicates that it is inappropriate both statistically and medically to use single markers as risk predictors when haplotype data are available, even when the mutation leading to the marker is identified as having a strong phenotypic association.
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