NOD Mice Substrain Divergence - Runs of Homozygosity

Divergence or rather Differentiation (to use the right terminology), between natural ecotypes or subspecies has been studied in multiple pairs. The broad-scale patterns and underlying processes for such genome wide changes has been studied in detail. 

Do similar processes govern the "divergence" of  artificially inbred strains? Is Drift too strong for background selection to be relevant in such inbred lines? Data [Genetic Analysis of Substrain Divergence in NOD Mice] from a recent study of NOD mice sub-strains might provide some answers. While the study was restricted to sites fixed to homozygosity, it does provide some idea of the major regions that differ between the mouse strains. More detailed analysis of the mouse strains including multiple individuals might be necessary to understand if the diversity landscape of the genome has played any role in shaping the accumulation of genetic differences. 

The Supplementary table 4 provides a list of all the SNP's genotyped using the Mouse Diversity Array. We try to identify runs of homozygosity that share the same genealogy and note if these regions correspond to the deletions identified and validated in the study.

Position				Variants
Chr	Pos (mm10)	Idd.region	SnpId	Type	BomTac	MrkTac	ShiJcl	ShiLtDvs	ShiLt
1	14207005		JAX00242533	G/C	G	G	G	C	C
1	39035554	Idd26	JAX00002691	T/-	T	T	-	T	T
1	39035867	Idd26	JAX00247792	C/-	C	C	-	C	C
1	39035916	Idd26	JAX00002693	A/-	A	A	-	A	A
1	39057575	Idd26	JAX00002694	C/-	C	C	-	C	C
1	111005763	Idd5.4a	JAX00262691	A/-	A	-	A	A	A
1	111014417	Idd5.4a	JAX00262692	T/-	T	-	T	T	T
1	111019979	Idd5.4a	JAX00262694	G/-	G	-	G	G	G
2	83392830		JAX00494876	G/-	-	-	G	-	G
2	131300866	Idd13, Idd13-not B2m	JAX00503778	A/G	A	A	A	G	A
3	8893755		JAX00514596	C/A	C	C	C	C	A
3	24286919		JAX00516977	C/-	C	C	C	-	-
3	24320030		JAX00516979	T/-	T	T	T	-	-
3	24348995		JAX00105316	A/G	A	A	A	-	-
3	24383100		JAX00516985	T/-	T	T	T	-	-
3	33847305		JAX00106024	-/G	G	G	-	G	G
3	33847927		JAX00519037	-/T	T	T	-	T	T
3	33848126		JAX00519038	-/A	A	A	-	A	A
3	33850816		JAX00519044	-/C	C	C	-	C	C
3	33851250		JAX00519045	A/-	A	A	-	A	A
3	33851593		JAX00519046	G/-	G	G	-	G	G
3	65332947		JAX00525208	T/C	T	T	T	T	C
4	44176075		JAX00549396	T/A	T	T	T	A	A
4	95778743		JAX00558533	G/A	G	G	G	A	G
5	22274118		JAX00575925	T/C	T	T	T	T	C
5	41404231		JAX00579937	T/-	T	-	T	T	T
5	66998537		JAX00584961	C/A	C	C	C	C	-
5	73358239		JAX00585757	C/T	C	C	C	T	T
6	38322613		JAX00607572	C/T	C	C	C	C	T
6	53666162		JAX00141075	C/-	T	T	-	T	T
6	61137631		JAX00611572	C/T	C	C	C	T	T
9	7195978		JAX00685032	A/G	A	A	A	G	G
9	29769301		JAX00688769	G/C	G	G	G	G	C
9	106903556		JAX00704737	G/A	G	G	G	G	A
11	3243750		JAX00023793	G/A	G	G	G	A	A
12	39375537		JAX00200149	G/-	G	-	G	G	G
13	116909804	Idd14	JAX00371636	G/A	G	G	G	G	A
15	32687601		JAX00397403	C/A	C	C	C	C	A
15	72708061		JAX00405386	G/A	G	G	G	G	A
16	29905094		JAX00416944	C/-	C	C	-	C	C
16	90657211		JAX00427835	G/A	G	G	G	A	A
18	58558824		JAX00460581	G/T	G	G	G	G	T
18	61847210		JAX00461436	G/A	G	G	G	G	A
18	66105915	Idd21.2	JAX00462793	G/A	G	G	G	A	A
18	84871118	Idd21.1	JAX00467924	-/T	T	T	-	-	-
19	50248464		JAX00479604	C/A	C	C	C	C	A
X	14217495		JAX00177287	C/A	C	C	C	A	A
X	101602508		JAX00716621	G/A	G	G	G	G	A

In the above table the runs of fixed differences and what they are is listed below:

1. First run (marked in blue) of fixed differences corresponds to the Idd26 locus.
2. Next is the Idd5 locus. 
3. The deletion on chromosome 3 spanning 24,272,052 and 24,383,100 has been validated by Sanger sequencing in this study.
4. The second deletion on chromosome 3 spanning as many as 6 SNP's is located rather close to the first deletion.

The remaining clusters of 2 or 3 sites that share the same genealogy are probably too short to correspond to single events themselves. Nonetheless, it would be interesting to see if these fixed differences are localized to lower nucleotide diversity regions in the initial strains.