Genome wide analyses reveal the population distinctiveness of the ‘Nera del Mela’ sheep

Figures & data

Figure 1. Pecora Nera del Mela sheep.

Table 1. Population’s full name (Name), acronyms (Code) and number of individuals after quality control of the 20 sheep populations included in the ITA and SIC datasets.

Name	Code	ITA	SIC
Nera del Mela	NER	36	36
Comisana	COM	24	24
Pinzirita	PIN	24	24
Sarda	SAR	24	24
Valle del Belice	VDB	24	24
Alpagota	ALP	24	–
Appenninica	APP	24	–
Bagnolese	BAG	23	–
Bergamasca	BER	24	–
Biellese	BIE	22	–
Delle Langhe	DEL	24	–
Fabrianese	FAB	23	–
Gentile di Puglia	GEP	24	–
Istrian Pramenka	IPR	24	–
Laticauda	LAT	24	–
Leccese	LEC	25	–
Massese	MAS	24	–
Sambucana	SAM	12	–
Sardinian Ancestral Black	SAB	20	–
Sopravissana	SOP	24	–

Table 2. Genetic diversity indices and run of homozygosity parameters for Nera del Mela sheep.

HO ± sd	HE ± sd	FIS ± sd	FROH ± sd	MAF ± sd	Ne	NROH ± sd	NCROH ± sd	LROH ± sd	LCROH ± sd
0.376 ± 0.149	0.370 ± 0.130	−0.017 ± 0.068	0.027 ± 0.053	0.283 ± 0.135	38.1	9.89 ± 16.49	13.69 ± 11.10	4.64 ± 3.00	6.34 ± 1.56

H_O: observed heterozygosity; H_E: expected heterozygosity; F_IS: inbreeding coefficient based on observed and expected heterozygosity; F_ROH: inbreeding coefficient based on run of homozygosity (ROH); MAF: average minor allele frequency; Ne: contemporary effective population size; N_ROH: mean number of ROH per individual; NC_ROH: mean number of ROH per chromosome; L_ROH: average length of ROH in Mb per individual; LC_ROH: average length of ROH in Mb per chromosome; sd: standard deviation.

Figure 2. Pairwise F_ST values estimated between the 20 Italian sheep populations (ITA dataset). For full definition of the dataset, see Table 1.

Figure 3. Multidimensional scaling analysis on the genotype data of the 20 Italian sheep populations (ITA dataset). For full definition of the dataset, see Table 1.

Figure 4. Neighbor-Joining Tree based on Allele Sharing Distances between the individuals of the 20 Italian populations of the ITA dataset. For full definition of the dataset, see Table 1.

Figure 5. Multidimensional scaling analysis on the genotype data of the 5 Sicilian populations (SIC dataset). For full definition of the dataset, see Table 1.

Figure 6. Neighbor-Joining Tree based on Allele Sharing Distances between the individuals of the 5 Sicilian populations (SIC dataset). For full definition of the dataset, see Table 1.

Figure 7. Circle plot of the ancestral clusters (K = 2–20) inferred by the Admixture analysis on the genotype data of the 20 Italian sheep populations (ITA dataset). For full definition of the dataset, see Table 1.

Data availability statement

The data that support the findings of this study are available upon request from the corresponding author.