An oligogenic architecture underlying ecological and reproductive divergence in sympatric populations
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary Biology, Germany
Figures
Figure 1
Population structure of the FM and NM types in Roscoff based on 721,000 genetic variants.
(A, B) Principal component analysis (PCA; A) and admixture analysis (B) identify one migrant in time (blue; pure NM genotype caught at full moon), many potential F1 hybrids (yellow) and four …
Figure 2 with 22 supplements
A complex inversion system on chromosome 1.
(A) Chromosome 1 harbors a block of markedly elevated genetic differentiation. (B) This genomic block coincides with two windows of elevated long-range LD in the FM and NM strains. (C) Structural …
Figure 2—figure supplement 1
Long-range linkage disequilibrium along chromosome 1.
Blocks of elevated genetic differentiation (A) correspond to blocks of elevated long-range LD in the FM type (B) and the NM type (C). Elevated long-range LD suggests that the inversion is …
Figure 2—figure supplement 2
Local admixture plots for the genomic windows corresponding to different inversions.
Gray bars and black bars represent the two classes of inversion homozygotes. Bars which are half black, half gray represent inversion heterozygotes. Support for In(1c) is not fully congruent with …
Figure 2—figure supplement 3
Genetic differentiation between homozygotes of the standard haplotype (SS) and inversion haplotypes (I1I1, I2I2).
Figure 2—figure supplement 4
Windowed PCA along chromosome 1, part 1 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 5
Windowed PCA along chromosome 1, part 2 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 6
Windowed PCA along chromosome 1, part 3 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 7
Windowed PCA along chromosome 1, part 4 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 8
Windowed PCA along chromosome 1, part 5 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 9
Windowed PCA along chromosome 1, part 6 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 10
Windowed PCA along chromosome 1, part 7 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 11
Windowed PCA along chromosome 1, part 8 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 12
Windowed PCA along chromosome 1, part 9 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 13
Windowed PCA along chromosome 1, part 10 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 14
Windowed PCA along chromosome 1, part 11 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 15
Windowed PCA along chromosome 1, part 12 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 16
Windowed PCA along chromosome 1, part 13 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 17
Windowed PCA along chromosome 1, part 14 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 18
Windowed PCA along chromosome 1, part 15 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 19
Windowed PCA along chromosome 1, part 16 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 20
Windowed PCA along chromosome 1, part 17 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 21
Windowed PCA along chromosome 1, part 18 (500kb sliding windows with 100 kb steps).
Figure 2—figure supplement 22
Windowed analysis for observed heterozygosity (A) and Admixture (B) along chromosome 1.
(A) A number of individuals (red arrows) show elevated heterozygosity beyond the end of In(1a). In three of them (individuals 38, 41, and 43), the ends of that region coincide (red lines). These …
Figure 3 with 1 supplement
Inversions in chromosomes 2 and 3.
(A) Chromosome arm 2L harbors a block of mildly elevated genetic differentiation. (B) Several blocks of long-range linkage disequilibrium (LD) point to additional inversions in the FM and NM …
Figure 3—figure supplement 1
Long-range linkage disequilibrium along chromosomes 2 and 3.
The block of slightly elevated genetic differentiation in chromosome arm 2L (A) correspond to a block of elevated long-range LD in the NM type (C), but not the full moon type (B). Blocks of elevated …
Figure 4
Lunar emergence time is heritable.
In a cross between FM type (A) and NM type (B), the F1 hybrids emerges intermediate between the parents (C). In the F2 (D), the phenotypes spread out again, but do not segregate completely, …
Figure 5 with 6 supplements
Quantitative trait loci (QTL) and genomic regions underlying FM vs NM emergence.
(A) Multiple QTL Mapping (MQM) identified four significant QTL controlling lunar emergence time. Confidence intervals were determined in MQM and Composite Interval Mapping (CIM). The marker order …
Figure 5—figure supplement 1
Scan for interacting QTL.
All chromosmes were scanned for interacting QTLs with the scantwo function of R/qtl. (A) For each possible QTL combination three models are tested, allowing for either additve and epistatic effects …
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Figure 5—figure supplement 1—source data 1
Table of test statistics for epistatic interactions.
- https://cdn.elifesciences.org/articles/82825/elife-82825-fig5-figsupp1-data1-v2.docx
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Figure 5—figure supplement 1—source data 2
Table of test statistics for additive interactions.
- https://cdn.elifesciences.org/articles/82825/elife-82825-fig5-figsupp1-data2-v2.docx
Figure 5—figure supplement 2
LOD profiles from Composite Interval Mapping (CIM).
(A) Backward selection models. (B) Forward selection models. CM = size of the exclusion window in centimorgan; COV = number of covariates. CIM generally identifies the same four QTL as MQM, but …
Figure 5—figure supplement 3
Inversion genotypes of the parents of the FMxNM cross.
Inversion genotypes were determined by local PCA for the inversions overlapping with detected QTL. For the FM type mother the inversion genotype of In(2R) is not clear. Inversion genotypes suggest …
Figure 5—figure supplement 4
Genotyping of an insertion-deletion in the period locus.
The NM strain is dominated by the long allele (L), the FM strain by the short allele (S).
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Figure 5—figure supplement 4—source data 1
Original gel pictures of the genotyping of an insertion-deletion in the period locus.
- https://cdn.elifesciences.org/articles/82825/elife-82825-fig5-figsupp4-data1-v2.zip
Figure 5—figure supplement 5
Gene models and genetic differentiation at the plum locus.
Dots are individual SNPs, the line is FST in 1 kb sliding windows with 200 bp steps. In the gene models, gray boxes are untranslated regions (UTRs), black boxes are coding sequence (CDS).
Figure 5—figure supplement 6
Gene models and genetic differentiation at the stat1 locus.
Dots are individual SNPs, the line is FST in 1 kb sliding windows with 200 bp steps. In the gene models, gray boxes are untranslated regions (UTRs), black boxes are coding sequence (CDS).
Additional files
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Supplementary file 1
Genome-wide structural variant (SV) calls.
- https://cdn.elifesciences.org/articles/82825/elife-82825-supp1-v2.zip
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Supplementary file 2
Inversion breakpoints as estimated from long range LD.
- https://cdn.elifesciences.org/articles/82825/elife-82825-supp2-v2.docx
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Supplementary file 3
Number of variants in inversion windows.
- https://cdn.elifesciences.org/articles/82825/elife-82825-supp3-v2.docx
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Supplementary file 4
Microsatellite and length polymorphism markers.
- https://cdn.elifesciences.org/articles/82825/elife-82825-supp4-v2.xlsx
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Supplementary file 5
Final QTL model as given by the fitqtl function, obtained with multiple imputation, a normal phenotype model and based on 158 observations.
- https://cdn.elifesciences.org/articles/82825/elife-82825-supp5-v2.docx
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Supplementary file 6
Peaks in genetic differentiation (FST).
- https://cdn.elifesciences.org/articles/82825/elife-82825-supp6-v2.xlsx
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Supplementary file 7
r/QTL input file.
- https://cdn.elifesciences.org/articles/82825/elife-82825-supp7-v2.csv
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MDAR checklist
- https://cdn.elifesciences.org/articles/82825/elife-82825-mdarchecklist1-v2.docx
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Source code 1
r/QTL script for QTL mapping.
- https://cdn.elifesciences.org/articles/82825/elife-82825-code1-v2.zip
