With K = 4, Brown Swiss and Holstein cattle were clearly separated, with the other three European populations showing intermediate levels of both ancestries.
Similar results were found in a mixed stand of Quercus lobata and Q. douglasii in North America: only one of the three individuals that showed the highest probability of hybrid ancestry (0.20 0.25) was intermediate in appearance [ 31].
a individual previously included in the phenotypically intermediate class b probability of mixed ancestry Values represent probabilities.
Nevertheless, 21 intermediate individual genotypes (more than 10% of ancestry coming from one of the 2 species) are counted: 3 F_spi and 18 F_ves.
However, plants with intermediate morphology did not show evidence of mixed ancestry more often than the plants with typical diffuse knapweed morphology.
Individuals were considered as intermediate genotypes when they have more than 10% of ancestry coming from one of the 2 species.
We interpret this as the result of conflicting signal from intermediate genotypes (for e.g., BM_BB or MM_BM) that have positive ancestry correlations.
In those South American groups European ancestry signals are usually high for NRY-DNA, intermediate for autosomal DNA, but low for mtDNA, whereas Native American genetic ancestry signals are reverse, indicating sex-bias admixture between mostly European men and mostly Native American women (Goncalves, et al., 2007; Corach, et al., 2010).
As expected, African-American samples (i.e. HapMap African Ancestry in Southwest, USA [ASW] and this study HUFS) show an LD structure intermediate to CEU and YRI (ESM Fig. 3 and ESM Fig. 2).
The distribution of NAT2 acetylator phenotypes (rapid, intermediate, and slow acetylators) between cases and control individuals was significantly different in the Mixed Ancestry group, while no significant difference was observed in the Black group, even when intermediate and slow acetylators were merged into one group and compared with the rapid acetylators (Table 3).
A concern has been whether the intermediate species branch in sister positions to C3 and C4 clades that would support a conclusion of shared ancestry and thus that the intermediate reflects an evolutionary transitional state [ 11, 17], however, resolving the phylogenetic positions of intermediates often requires a data-rich phylogeny [ 18].
