Table 3. Synteny between lake trout linkage groups and Arctic char, rainbow trout, Atlantic salmon, and brook trout genomes. Arctic char, rainbow trout, and Atlantic salmon chromosomes were recorded if more than 50 RAD contigs from the lake trout linkage group were aligned to a chromosome with a mapping quality of 60. Brook trout linkage groups were recorded if more than 10 aligned markers were detected by MapComp. Graphical depictions of alignment location vs. linkage map position are available in Supplementary Figures S1-S7.

Lake Trout	Arctic Char	Rainbow Trout	Atlantic Salmon	Brook Trout
Sna1	Sal15	Omy6	Ssa24, Ssa26	BC6
Sna2	Sal1	Omy17	Ssa12	BC3
Sna3	Sal20	Omy12	Ssa03, Ssa13	BC8, BC14
Sna4	Sal18	Omy16, Omy23	Ssa01, Ssa19	BC1
Sna5	Sal6.1, Sal6.2	Omy2, Omy14	Ssa05	BC7
Sna6	Sal3	Omy21	Ssa07	BC2
Sna7	Sal27	Omy15, Omy18	Ssa16, Ssa29	BC5
Sna8	Sal13	Omy4, Omy10	Ssa04, Ssa23	BC4
Sna9	Sal26	Omy1	Ssa16	BC20
Sna10	Sal16	Omy5	Ssa10	BC17
Sna11	Sal32	Omy8	Ssa14	BC22
Sna12	Sal23	Omy10	Ssa04	BC9
Sna13	Sal2	Omy3	Ssa25	BC24
Sna14	Sal7	Omy9	Ssa15	BC30
Sna15	Sal9	Omy19	Ssa01	BC12
Sna16	Sal17	Omy16, Omy20	Ssa13, Ssa19	BC18
Sna17	Sal8	Omy25	Ssa09	BC33
Sna18	Sal33	Omy11	Ssa20	BC40
Sna19	Sal36	Omy22	Ssa21	BC26
Sna20	Sal11	Omy7	Ssa22	BC21
Sna21	Sal4q.1:29	Omy2	Ssa10	BC15
Sna22	Sal25	Omy1	Ssa18	BC36
Sna23	Sal22	Omy27	Ssa20	BC25
Sna24	Sal14	Omy4	Ssa06	BC31
Sna25	Sal19	Omy28	Ssa03	BC11
Sna26	Sal5	Omy29	Ssa11	BC10
Sna27	Sal31	Omy18	Ssa27	BC23
Sna28	Sal4q.2	Omy25	Ssa09	BC35
Sna29	Sal28	Omy8	Ssa15	BC19
Sna30	Sal10	Omy26	Ssa11	BC28
Sna31	Sal4q.1:29	Omy5	Ssa01	BC13
Sna32	Sal30	Omy14	Ssa14	BC34
Sna33	Sal14	Omy11	Ssa19	BC16
Sna34	Sal4p	Omy24	Ssa09	BC38
Sna35	Sal8	Omy20	Ssa28	BC27
Sna36	Sal37	Omy9	Ssa18	BC32
Sna37	Sal35	Omy3	Ssa02	BC29
Sna38	Sal24	Omy15	Ssa17	BC37
Sna39	Sal21	Omy13	Ssa02	BC42
Sna40	Sal12	Omy7	Ssa17	BC39
Sna41	Sal20	Omy13	Ssa06	BC14
Sna42	Sal34a	Omy19	Ssa08	BC41

^aSal34 appears to be homologous with Sna42, however fewer than 50 RAD contigs mapped to this chromosome.