Recombination frequency relative to the centromere (R) at loci toward the distal end of Chromosome 4 approaches 50% (Table 4), and at locus 3054 and beyond (including the sequenced region tim) insignificant LOD scores for linkage between the markers and the centromere were obtained; therefore statistically, these loci assorted independently of the centromere in this limited sample of chromosomes.
Inbred strains represent thus essentially a random sample of chromosomes drawn from specific wild populations or admixed from various origins.
Samples of chromosomes 2H – 7H where 60,000 purified chromosomes were used as a template provided lower amplification bias compared with those of 1H where only 10,000 chromosomes were used.
It is important to note that the expected values of neutrality statistics like those used here are not the same for both a random sample of chromosomes and a partitioned subset of chromosomes.
For the coalescent simulations with heterogeneous recombination rates, we used msHOT [ 56], a modification of [ 53] coalescent-based program (ms) for simulating genetic variation data for a sample of chromosomes from a population.
Much of our knowledge about the patterns of ME insertion variation, especially in humans, has been collected by first ascertaining polymorphic ME insertion loci in a small sample of chromosomes and then genotyping those loci in a larger sample from the population (e.g., [ 3- 5]).
Thus each individual is produced by selfing with probability 1/ N. Due to the added structure in which each gamete contains two distinct parental copies of each locus, and in contrast to the diploid monoecious case, samples of chromosomes from a tetraploid species are not exchangeable.
Gene order comparisons were made using the SPRING web server [ 51], which takes a sample of chromosome gene orders and orientations as its input and then computes a minimum series of reversals and/or block-interchanges necessary for transforming each chromosome into every other chromosome.
The second problem is that haplotypes become increasingly unique when markers are located on regions more distant on the genome due to occurrence of recombinations and random sampling of independent chromosomes.
Worldwide population sampling of Y-chromosomes reveals a phylogeny with the deepest divergences within African populations and all non-Africans closely related and restricted to a single branch of the tree (Hammer et al. 1998; Underhill et al. 2000).
