How do introgression events shape the partitioning of diversity among breeds: a case study in sheep

Leroy, Grégoire; Danchin-Burge, Coralie; Palhière, Isabelle; SanCristobal, Magali; Nédélec, Yann; Verrier, Etienne; Rognon, Xavier

doi:10.1186/s12711-015-0131-7

Genetics Selection Evolution

Table 2 Summary of genetic diversity measures across the 51 populations

From: How do introgression events shape the partitioning of diversity among breeds: a case study in sheep

Breed code	He	Ho	MNA	Ae	Ar (N ≥ 18)	F_IS	Excess HWE	Deficiency HWE	Assignement (%) (Bayesian clustering)
AuCa	0.70	0.72	7.81	4.31	6.72	−0.019			91.2
Avra	0.52	0.54	4.57	2.72	4.28	−0.035			100
BaBe	0.71	0.72	7.05	3.98	6.15	−0.012			100
Bare	0.72	0.71	7.43	4.77	-	0.015			-^a
BeCh	0.55	0.57	4.91	2.84	4.45	−0.038			97.5
BeIl	0.48	0.50	3.62	2.14	3.40	−0.042			100
BeIn	0.65	0.65	6.19	3.58	5.42	0.001			100
Bize	0.65	0.64	5.81	3.62	5.36	0.024			100
BlMa	0.56	0.56	5.24	2.76	4.53	0.003		1	90.5^f
BlMC	0.72	0.73	8.14	4.45	-	−0.017			62.5
Boul	0.65	0.65	5.48	3.51	5.02	−0.006			97.5
CaLo	0.62	0.60	5.86	3.30	5.25	0.029			100
Cast	0.71	0.71	6.24	4.38	5.99	0.008			76.9
Char	0.54	0.55	4.62	2.49	4.25	−0.019			100
Cors	0.76	0.75	8.48	5.18	7.72	0.013			77.8
Cote	0.53	0.53	4.29	2.56	3.93	−0.016		1	100
DoDo	0.67	0.63	6.10	3.71	5.99	0.060			60
EsLM	0.71	0.73	6.95	4.20	6.14	−0.024			95
Griv	0.71	0.71	7.76	4.23	6.63	0.003			100
Hamp	0.67	0.66	6.05	3.59	5.55	0.016			94.9^e
IlFr	0.66	0.66	5.52	3.60	5.10	−0.006			100
LaBr	0.55	0.49	4.71	2.43	4.26	0.117**		1	96.7^b
LaLC	0.69	0.68	7.00	3.90	6.02	0.020			50
LaLO	0.67	0.69	6.71	3.66	5.82	−0.031			77.5
LaVG	0.69	0.69	6.67	3.87	5.75	−0.001			92.5
LaVO	0.71	0.72	7.91	4.25	6.79	−0.021			65
Land	0.68	0.69	5.57	3.44	5.10	−0.014			93.1
Limo	0.72	0.72	7.33	4.45	6.44	−0.014		1	91.2
Lour	0.71	0.74	7.24	4.48	6.48	−0.039			76.5
MaTN	0.71	0.71	6.91	4.31	6.23	0.004	1		100
MaTR	0.72	0.69	6.86	3.94	6.04	0.027			85
MeAr	0.74	0.75	8.10	4.38	6.90	−0.011			80
MeRa	0.50	0.50	3.05	2.32	2.96	0.005			100
MoCh	0.66	0.64	6.67	3.55	5.75	0.028			97.5^c
MoNo	0.70	0.71	7.24	3.72	6.11	−0.010		1	78.4^b
Mour	0.70	0.70	7.67	3.97	6.54	−0.004			74.3^b
MoVe	0.61	0.60	6.33	3.14	5.49	0.010			100
NoVe	0.72	0.70	8.19	4.67	7.05	0.044			84.4
PrSu	0.71	0.68	7.81	4.13	6.61	0.034			90
Rava	0.69	0.72	6.95	3.89	6.15	−0.058*			89.7
RoHa	0.58	0.58	5.71	2.72	4.76	−0.010			98.2
Roma	0.70	0.71	6.95	3.98	6.21	−0.002			100^d
RoOu	0.61	0.60	6.38	3.20	5.35	0.018			95.7^f
Roov	0.61	0.61	4.33	3.01	-	0.005			100^d
RoRo	0.72	0.76	7.71	4.35	6.89	−0.055			86.7
Solo	0.60	0.60	4.62	2.91	4.20	−0.012			100
Sout	0.57	0.59	4.38	2.66	4.30	−0.030			100^c
Suff	0.61	0.59	5.14	3.13	4.55	0.027			100^e
Tara	0.71	0.70	8.05	4.02	7.04	0.016			46.9
Texe	0.65	0.66	5.62	3.14	4.86	−0.012			100
ThMa	0.69	0.68	7.10	4.18	6.06	0.014			97.4

He = non-biased expected heterozygosity; Ho = observed heterozygosity; MNA = mean number of alleles per locus; Ae = effective number of alleles per locus; Ar (N ≥ 18) = allelic richness computed for populations with more than 18 individuals genotyped for each locus; F _IS* = significant value after sequential Bonferroni correction (test significance: * P < 0.05. ** P < 0.01); Deficiency HWE/Excess HWE = number of Loci in Heterozygote Deficiency/Excess, after sequential Bonferroni correction; ^anever more than two individuals clustered together; ^bthe breed is associated with two different private clusters (see text); ^c,d,e,fresults are provided considering the cluster shared by the two breeds for K = 51; these two breeds were however clearly segregated when analyzed separately (see text)

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ISSN: 1297-9686

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