Table 1. Major loci likely contributing to the selection response.

These eight loci show significant allele frequency shifts in ∆z² and are ordered according to their estimated selection coefficients according to Haldane (1932). Shown for each locus are the full hitchhiking spans, peak location and their size covering the core windows, the overlapping TAD and the number of genes found in it. The two top-ranked loci show shifts in parallel in both LS1 and LS2, with the remaining six showing line-specific response (LS1: 1; LS2: 5). Candidate genes found within the TAD with limb, cartilage, or bone developmental knockout phenotype functions are shown, with asterisks (*) marking those with a ‘short tibia’ knockout phenotype (see also Figure 2—figure supplement 3 and Supplementary file 3 for full table).

Rk	Chr	Span (Mbp)	Peak	Core (kbp)	TAD (kbp)	Genes	∆q
							LS1	LS2	Ctrl	Type	Candidate genes
1	5	38.95–45.13	41.77	900	720	3	0.69	0.86	−0.14	Parallel	Nkx3-2
2	10	77.47–87.69	81.07	5360	6520	175	0.79	0.88	−0.04	Parallel	Sbno5, Aes, Adamtsl5*, Chst11*, Cry1, Prdm4*
3	18	53.63–63.50	58.18	220	520	4	0.05	0.78	−0.06	LS2-specific	-
4	13	35.59–55.21	48.65	70	2600	22	0.24	0.80	−0.03	LS2-specific	Id4
5	1	53.16–57.13	55.27	10	720	4	0.65	0.01	−0.23	LS1-specific	-
6	15	31.92–44.43	41.54	10	680	3	−0.23	0.66	0.02	LS2-specific	Rspo2*
7	6	118.65–125.25	120.30	130	1360	12	−0.03	0.79	−0.15	LS2-specific	Wnt5b*
8	11	111.10–115.06	113.42	10	2120	2	−0.14	0.66	−0.15	LS2-specific	Sox9*

Rk, Rank.

Chr, Chromosome.

Core, Span of 10 kbp windows above H_{INF, max LD} p≤0.05 significance threshold.

TAD, Merged span of topologically associating domains (TAD) overlapping the core span. TADs mark segments along a chromosome that share a common regulatory mechanism. Data from Dixon et al. (2012).

Candidate genes, Genes within the TAD span showing ‘short tibia’, ‘short limbs’, ‘abnormal osteoblast morphology’ or ‘abnormal cartilage morphology’ knockout phenotypes are listed, with * marking those with ‘short tibia’.