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In models with maximum genetic divergence, subpopulations were fixed for different alleles at each locus.
The diameter of the circle represents the maximum genetic divergence between any pair of sequences within a sample.
For the dataset comprising the three nidovirus-wide conserved proteins (Fig. 3ac), Miniopterus bat coronavirus 1 also showed a maximum genetic divergence exceeding that of the CAVV-NDiV pair.
However, some LD was detected when the lower rate of gene exchange and maximum levels of genetic divergence between chromosome arrangements was used, with 82.6% (mean r = 0.36) of alleles showing a significant association with the inversion for simulations started at maximum genetic divergence between chromosome arrangements.
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The maximum K2P genetic divergence between haplotypes was of 7.6% (between H61 and H69).
*Multiple sequences were chosen to capture the maximum extent of intraspecific genetic divergence within highly diverse taxa (variants arbitrarily labeled A or B).
Spatial autocorrelation analysis with Alleles in Space (AIS), for the whole species, agrees with the above result, but showed a direct correlation between genetic and geographic distances up to approximately 230 km, after that the genetic divergence is maximum and shows no further increase (data not shown).
Three lineages (100% bootstrap and 7% overall divergence) were identified using a maximum likelihood phylogenetic analysis which showed high genetic divergence (17.2 22.7%).
Genetic divergence among ITS types averaged 4% (maximum pairwise divergence was 13%).
High haplotype (Hd) diversity (Hd = 0.871) contrasts with low nucleotide diversity and little genetic divergence between haplotypes (π = 0.00951; maximum number of pairwise differences between haplotypes = 9).
Based on percentage of genetic divergence of this F gene fragment, the maximum intra-genotype nucleotide variations within any old genotype (below 7%) is lower than the minimum nucleotide distance found between these genotypes and the MG group (12% to 25%).
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