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To test these hypotheses, we first reconstructed the species' phylogeographic history, and second, we measured the shell sizes of extant individuals throughout South Africa.
The sample fraction was 20% of extant individuals (780 total) and sampling was random without replacement.
Reconstructability of population history, from genetic information of extant individuals, is studied under a simulation setting.
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The main idea of ARG-walker is to estimate, through analysis of ARG topology, the frequencies of historical recombinations, which are then used to approximate the recombination propensities of extant individual chromosomes.
The pedigree consists of 184 extant individuals, or individuals of the most current generation, and a family of size 456 with three generations.
FastDate analyses were run with time discretized into 1,000 intervals and the ratio of sampled extant individuals set to 0.14.
Assume that the characteristics of a population can be derived, say from the linkage disequilibrium landscape and other characteristics of observed extant individuals.
The underlying mutations are known for all four diseases, and genotyping data of the 1642 extant individuals confirmed the presence of homozygote(s) of the disease-causing mutations for the first three diseases (Chong et al. 2012).
For the other three diseases, genotype data of the 1642 extant individuals confirmed the presence of an individual(s) homozygous for the disease allele in the pedigree (Chong et al. 2012).
The depth of the extant individual is defined to be zero and the value progressively increases as one traverses the ARG away from the terminal leaf nodes.
These hotspots are estimated from patterns of linkage disequilibrium (LD) between extant individuals, reflecting recombination occurring throughout their ancestral lineage [26].
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