Jacobs et al. Supplementary material
The genetic architecture underlying the evolution of a rare piscivorous life history form in brown trout after secondary contact and strong introgression.
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GRU LNF benthiv. brown MCF trout SLA KER - ferox
Figure S1. Neighbour-joining network based on 16,066 SNPs.
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Figure S2. Folded site-frequency spectrum for ferox trout (FE) and combined benthivorous brown trout (BR).
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chr21 chr29 benthiv. trout 6 ferox trout
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Figure S3. Genome scan of nucleotide diversity (π) across each chromosome for benthivorous brown trout (brown line) and ferox trout (orange line). Genomic islands of divergence are marked with red bars.
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A chr1 chr10
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0.00 Haplotype diversity chr21 chr29 benthiv. trout ferox trout 0.75
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Figure S4. Genome scan of gene diversity and haplotype diversity, both calculated based on haplotype-information derived from full RAD loci. Genomic islands of divergence are marked with red bars.
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chr1 chr10
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reduced diversity in benthivorous brown trout gene diversity reduced diversity in ferox trout haplotype diversity
Figure S5. Delta haplotype and gene diversity across the Atlantic salmon genome. Negative delta diversity shows reduced diversity in benthivorous brown trout compared to ferox trout, whereas positive delta diversity shows reduced diversity in ferox trout. Genomic islands are highlighted with red bars. Brown and orange arrow heads highlight genomic islands with reduced diversity in benthivorous brown trout or ferox trout, respectively.
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A 50 B
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Weir and Cockerham Fst 0.0 1234567 9 101112 13 14 15 16 17 19 20 21 23 25 27 29 Chromosome
Figure S6. Fst distribution across the genome. A) Genome-wide distribution of Fst-values. Top 5% Fst-outlier loci are highlighted in red. B) Fst-value distribution of top 5% Fst-outlier loci. C) Distribution of Fst-values across the Atlantic salmon genome. Loci are alternatingly coloured by chromosome.
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A chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8
2.5 0.0 -2.5 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16
2.5 0.0 -2.5 chr17 chr18 chr19 chr20 chr21 chr22 chr23 chr24 ZFst
2.5 0.0 -2.5 chr25 chr26 chr27 chr28 chr29 GRU vs. Kernsary ferox LNF vs. Kernsary ferox MCF vs. Kernsary ferox 2.5 0.0 -2.5
B GRU vs. KER LNF vs. KER MCF vs. KER 8000 10000
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0 0 0 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00
Genetic differentiation (Fst)
Figure S7. A) Genetic differentiation (loess-smoothed window-based ZFst) across the Atlantic salmon genome for sampling site specific comparisons. Red bars highlight genomic islands identified in the combined genome scan. B) Genome-wide distribution of Fst-values (on a SNP basis) by sampling site.
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Table S1. Model selection of the most likely demographic model for the reduced dataset.
Model ln(lhood) 1 N.parameters AIC ∆AIC SCadm -85481.55 8 170979.1 0.0 IMchange -85486.90 7 170987.8 8.7 SC -85504.60 6 171021.2 42.1 IM -85506.77 5 171023.5 44.4 AM -85506.88 6 171025.8 46.7 SI -85776.11 4 171560.2 581.1 Table legend: 1ln(likelihood), AIC: Aike information criterion.
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Table S2. GO-terms (biological processes) associated with genes within genomic islands. No GO-term was significantly overrepresented (FDR < 0.05). GO-term Description Fold enriched P-value FDR Gene names GO:0055085 transmembrane transport 2.85 0.0013 1 atp6v1d;mmgt1;slc25a40;slc37a1;slc7a2;slc39a9;chrna5;cyc1;gabrp ;chrnb4;grik5 GO:0006401 RNA catabolic process 10.44 0.0029 1 rnaseh1;smg8;cnot7 GO:0034220 ion transmembrane transport 3.09 0.0039 1 mmgt1;slc7a2;slc39a9;chrna5;cyc1;gabrp;chrnb4;grik5 GO:0006810 transport 1.91 0.0048 1 atp6v1d;ergic3;mmgt1;chmp3;slc25a40;slc37a1;slc7a2;slc39a9;ccs; chrna5;ap5s1;cyc1;syt12;gabrp;pom121;chrnb4;grik5 GO:0051234 establishment of localization 1.87 0.0060 1 atp6v1d;ergic3;mmgt1;chmp3;slc25a40;slc37a1;slc7a2;slc39a9;ccs; chrna5;ap5s1;cyc1;syt12;gabrp;pom121;chrnb4;grik5 GO:0006811 ion transport 2.61 0.0068 1 mmgt1;slc7a2;slc39a9;ccs;chrna5;cyc1;gabrp;chrnb4;grik5 GO:0007179 transforming growth factor 13.41 0.0096 1 smad5;smad9 beta receptor signaling pathway GO:0071559 response to transforming 13.41 0.0096 1 smad5;smad9 growth factor beta GO:0071560 cellular response to 13.41 0.0096 1 smad5;smad9 transforming growth factor beta stimulus GO:0010629 negative regulation of gene 3.82 0.0097 1 eif4ebp2;smad9;cnot7;brms1la;nrde2 expression
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Table S3. KEGG pathways (Danio rerio) associated with genes within genomic islands. No KEGG pathway was significantly overrepresented (FDR < 0.05). KEGG pathway Description Fold enriched P-value FDR Gene names dre04110 Cell cycle 3.406 0.0569 1 e2f1;ccne1;dbf4 dre04068 FoxO signaling pathway 2.749 0.0944 1 cat;pik3r5;agap2 dre04146 Peroxisome 3.561 0.1079 1 cat;crot dre04080 Neuroactive ligand-receptor interaction 1.929 0.1132 1 lpar1;chrna5;gabrp;chrnb4;grik5 dre00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis 6.812 0.1372 1 pigu dre04350 TGF-beta signaling pathway 3.072 0.1375 1 smad5;smad9 dre00515 Mannose type O-glycan biosynthesis 6.528 0.1427 1 b4gat1 dre04012 ErbB signaling pathway 2.798 0.1596 1 pik3r5;camk2b dre00514 Other types of O-glycan biosynthesis 5.402 0.1699 1 colgalt1 dre04144 Endocytosis 1.832 0.1716 1 agap1;chmp3;cav2;agap2
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Table S4. Genes associated with loci putatively under selection. Chromosome Start End Annotation AS100 SNP position Gene name NC_027300.1 72268063 73360509 macrod2 72742754 MACRO Domain Containing 2 NC_027301.1 48437588 48465607 LOC106587077 48444034 phosphoinositide 3-kinase regulatory subunit 5-like NC_027306.1 1182340 1211964 LOC106608430 1191948 toll-like receptor 2 NC_027308.1 41684365 41709169 LOC106611358 41703379 potassium channel subfamily K member 2-like NC_027312.1 35989028 36000630 LOC106567076 35989910 phosphatidylinositol 5-phosphate 4-kinase type-2 gamma NC_027314.1 69288197 69426575 LOC100380856 69438241 thymocyte selection-associated high mobility group box protein TOX NC_027316.1 31048572 31051812 LOC106575965 31040284 submaxillary mucin-like protein NC_027320.1 18801789 18803016 Transmembrane 18800138 Transmembrane protein 50B NC_027320.1 18894788 18901571 LOC106581898 18865196 ribosomal RNA processing protein 1 homolog B-like NC_027320.1 21137945 21315616 LOC106581930 21291538 PTB domain-containing engulfment adapter protein 1 NC_027321.1 13654002 13783467 LOC106582849 13766129 E3 ubiquitin-protein ligase PDZRN3-like NC_027324.1 32744589 32876560 LOC106586624 32836501 immunoglobulin superfamily member 3-like
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