Although this is not reflective of nuclear population structure (Fig. 3C), it suggests that even for elephants from localities that shared some haplotypes, sets of elephants might be distinguished by differences in haplotype frequencies (Fig. 5, Table S6).
Our findings indicate differentiated demographic aggregations of breeding individuals in these two stocks with small evolutionary divergence, as evidenced by significant differences in haplotype frequencies, coupled with small and non-significant molecular distances and high migration rates.
Such an effect could be explained by a simple global inversion of ~5 Mb in the haplotype 4311 or by differences in the sequence of the different haplotypes.
These different abnormalities between mice with two backgrounds may have been caused by differences in their H-2 haplotype (C57BL/6; b, DBA/1J; q).
There were no differences in haplotypes within the clades, with the exception of M059, which differed by a single base pair from other M. capitata samples.
The limited success of across breed imputation from 50 k to HD is most likely caused by differences in LD phase and thus haplotype dissimilarity across breeds on the 50 k panel [ 8, 11], but the greater marker density on the HD panel might alleviate these differences for diverged breeds [ 12], meaning that across breed imputation could be successful from HD to whole genome sequence data [ 11].
We were able to identify three distinct structural haplotypes characterized by differences in copy-number and arrangement of the LCR22-2 genes and pseudogenes.
Furthermore, by taking advantage of differences in haplotype structure, populations of different ancestries can help to narrow down loci, thereby pinpointing causal genes for functional follow-up.
If any lineage is indeed a genuine tracer of Neolithic diffusion from Anatolia, 1) it must be present in the recipient populations and 2) when present its intra-haplotype variation defined by differences in length of the STRs should be a proper subset of that observed in Anatolia.
Estimated haplotype variance was hardly affected by differences in window size or limitIBD.
