Allelic frequency change
We sequenced between 53 and 74 million reads per pool (BioProject XXXX).
After quality trimming and mapping, this sequencing effort resulted in
an average coverage of 31.9x (SC mtDNA) and 41.1x (SD mtDNA) for the
initial F2 hybrids, 33.9x, 43.1x and 35.4x for the lines evolving under
the SC mitochondria, and 33.5x, 33.5x and 34.5x for the lines evolving
under the SD mitochondria. After reciprocal mapping to the reference
genomes of both parental populations and filtering for fixed SNPs, our
approach allowed us to estimate read counts for 1,658,000 ancestry
informative SNPs, corresponding to 3,316 genomic windows, and covering
the 12 chromosomes of T. californicus .
The allelic frequencies in adult F2 were generally close to 50% (Figure
S2), varying between 38 and 64% in the F2s with the SC mitochondria,
and between 34 and 61% in the F2s with the SD mitochondria. This
variation was relatively stable along each of the 12 chromosomes,
consistent with chromosome-wide linkage disequilibrium. In contrast,
allelic frequencies in hybrid lines after experimental evolution showed
a strong deviation from 50% (Figure S3). This deviation was most
pronounced in the lines evolving under the SC mitochondrial background,
where the frequency of the SD allele ranged between 5 and 90%. The
lines evolving under the SD mitochondrial background showed a more
modest allele frequency change, ranging from 20 and 76% for the SD
allele. Contrary to F2s, changes in allelic frequency were variable
along each of the 12 chromosomes, showing that the effective population
recombination rate was enough to reduce linkage disequilibria during the
nine months of experimental evolution.
The SC lines showed the most extreme P-values of rejecting the null
hypothesis of no allelic frequency change, with genomic windows reaching
the threshold of -log10 (P-value) =1.73 in all 12 chromosomes. Larger
genomic regions were identified in 8 chromosomes, 7 of which favored the
nuclear allele matching the mitochondrial background (i.e. SC allele).
The only region in which the opposite allele was favored (i.e. SD allele
in chromosome 11) did not show a similar pattern in lines evolving under
the SD mitochondria. The SD lines showed less extreme P-values
supporting allelic frequency change, with genomic windows above the
threshold located in 6 chromosomes. Larger genomic regions were
identified in 5 chromosomes, 3 of which favored the nuclear allele
matching the mitochondrial background (i.e. SD allele). Notably, the
chromosomal regions in which the opposite parental allele was favored
(i.e. SC allele in chromosomes 7 and 8), show a similar pattern in the
SC lines. Genomic regions responding to selection varied between 62 Kbp
– 6.2 Mbp for the SC lines and 512 Kbp – 3.2 Mbp for the SD lines.
From the 3,316 genomic windows analyzed here, 60.5% were not skewed in
both lines and occurred in all 12 chromosomes, consistent with a
prevalent role of genetic drift. About 6.5% of the windows shows a
consistent skew towards the SC allele, mostly in chromosome 7 and in
part of chromosome 8, consistent with uniform selection favoring SC
alleles. The SD alleles were never consistently favored in both
mitochondrial backgrounds. The remaining 33% of the genome show skews
dependent on the mitochondrial background and are therefore consistent
with divergent selection.
Of the 909 genomic windows that are skewed only in the SC mitochondrial
background, 88.6% show a skew favoring the matching SC nuclear allele,
in chromosomes 2, 3, 8,10 and 12. The remaining 11.4%, all in
chromosome 11, show a skew towards the mismatched SD nuclear allele. Of
the 187 genomic windows that are skewed only in the SD mitochondrial
background, 87% show a skew towards the matching SD nuclear allele, in
chromosomes 4, 6, and 9. The remaining 13% show a skew towards the
mismatching SC nuclear allele, but notably all these windows are
adjacent to windows likely under uniform selection favoring the same
allele in chromosome 7.