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One possible issue with using the criterion of mutual allelic exclusivity to delineate species is that populations inhabiting contrasting environment can have distinct alleles at loci that are differentially selected: for such markers under selection, one may then end up with sl-FFRs that are less encompassing than the real species as they rather delineate intra-specific ecological niches.
However, when considering percentage rather than total number of markers under selection, results were similar.
This criterion produced one set of 4810 neutral markers and 167 markers under selection.
The three approaches handle the detection of markers under selection in a different manner and are expected to produce slightly different results.
In order to eliminate markers under selection for the subsequent genetic analyses, we performed an outlier detection using BayeScan software [ 32].
Since each of the five tests used above relies on somewhat different assumptions, loci that are repeatedly found to be outside the range expected for neutrality are extremely good candidates for markers under selection.
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Markers affected by selection are then expected to display an unexpectedly high or low value relative to the null distribution of FST for markers not under selection.
Three subsets of data were constructed: the first with 155 PN AFLPs (with 145 markers falling within the expected distribution at P < 0·05 and 10 with a significantly lower FST than expected) and the second and the third with markers putatively under selection at P < 0·05 (PS0·05) and P < 0·01 (PS0·01), consisting of 95 and 76 AFLPs, respectively.
Indeed, the frequency of markers putatively under selection PS0·01 was significantly higher for loci linked to genes and QTLs involved in the domestication process, compared with the other parts of the genome, and PS0·01 showed a significantly smaller distance from domestication QTLs compared with PN.
Specifically, population divergence should be less for markers under balancing selection, in comparison with neutral markers, because of the greater effective migration rate of alleles under balancing selection (Scheierup et al. 2000).
The remaining 5 AJ markers under SSPI selection gave unreadable sequence data.
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