Separate GST values were calculated for markers linked to each of the inversion haplotypes and ecological loci, and for markers unlinked to loci under selection (neutral loci).
Ecological selection in the hybrid habitat favoured the intermediate genotypic value that is found in the two novel homozygotes and the double heterozygote at the two ecological loci.
However, hybrid speciation via recombination at both inversion haplotypes and ecological loci was far more common than via recombination at inversion haplotypes alone.
Separate GST values were based on marker loci completely linked to the two ecological loci and to the two inversion haplotypes, and on two unlinked markers that segregated independently of all loci under selection.
When ecological selection is weak, individuals with the parental karyotypes are able to survive in the hybrid zone at a relatively high rate, and as a result, introgression at ecological loci is the common outcome under these conditions.
The decay in GST was similar for markers linked to ecological loci and inversion haplotypes, whereas values for markers that were not linked to loci under selection declined more rapidly and to lower values after 1000 generations.
This is probably because substantial ecological selection was necessary for hybrid speciation to occur and as a result multilocus associations usually built up between inversion haplotypes and ecological loci.
The genomes of these prokaryotes are assumed to consist of three types of loci: (i) loci involved in the adaptation to the new niche (E or ecological loci, for short), (ii) n loci subject to NFDS (S or susceptibility loci, for short), and (iii) all the other loci, which are assumed to be neutral (N or neutral loci, for short; only one such locus is shown in Figure 2a).
We suggest that the subspecies A. l. farallonensis be recognized only if other data (from morphological, ecological, or multi-locus genetic studies) should prove to be concordant with the mtDNA results.
At later stages of ecological speciation, as many loci diverge among incipient species, genome-wide effective gene flow will be reduced even at unlinked loci: divergence hitchhiking being superseded by genome hitchhiking (GH) [ 16].
