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All putative cutthroat smolts were also genotyped for these four diagnostic loci (genetic data available by request).
The E and the Z races are known to share a large amount of polymorphism at allozyme [38], [39], [41], [42] and DNA [40] level, but also to differ at two diagnostic loci in addition to Pher: Olf [22], [26] and Resp [22], [25], [27].
Adding two known diagnostic loci to the set made negligible difference.
Hence, each line could have a different combination of diagnostic loci that border intervals of varying lengths.
Twenty CanSINE loci were diagnostic for internal clades within Felidae while seven of the eight major felid lineages had diagnostic loci.
Strains that differed in nucleotide sequence from any of the >3000 MLST-typed E. coli at any of the three diagnostic loci were deemed as " unique" and stored in LB broth supplemented with 15% glycerol and stored at −80°C.
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One intraspecific diagnostic locus (L16*) showed discriminating alleles between Kashmir and Quebec, and could be useful to determine whether individuals introduced outside of the native range are from similar or different source populations in the native range.
Finally, to assess the impact of having just a few known diagnostic markers, I repeated this analysis replacing one locus of each type with a diagnostic locus, and performed estimation assuming those two were diagnostic but still assuming the other 48 markers had allele frequencies of 0.8 and 0.2.
We aimed at comparing the performance of network and Bayesian coalescent analysis (STRUCTURE, [ 16]) to test whether the shared polymorphism and the absence of diagnostic locus was mainly due to retained ancestral polymorphism, or to present day hybridization in sympatric zone.
Following this screening exercise, the three species-diagnostic loci were removed from the data set.
These reads should be perfectly aligned to the donor genome, and the transcripts should meet at least one of the following criteria: (1) having at least one read carrying two or more diagnostic SNP loci (Fig. 1a); (2) having at least two unique reads covering one diagnostic SNP locus (Fig. 1b); or (3) having two or more unique reads carrying different diagnostic SNP loci (Fig. 1c).
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