Genetic Diversity and Variability in two Italian Autochthonous Donkey Genetic Types Assessed by Microsatellite Markers

Figures & data

Table

Run	K	LnP(D)	Var[LnP(D)]	SD	L’(K)=L(K)–L(K-1)	IL”(K)=L’(K+1)-L’(K)	AK=m(IL”(K)I)/s[L(K)]
1	2	-5412.7	113.7	10.663
2	2	-5413.3	114.7	10.710
3	2	-5412.8	113.7	10.663
4	2	-5413.1	114.5	10.700
5	2	-5413.3	114.7	10.710
Mean value		-5413.04	114.26	10.689
1	3	-5325.5	190.2	13.791
2	3	-5453.4	440.9	20.998
3	3	-5326.5	192.6	13.878	61.72	-0.28	-0.018351285
4	3	-5326.8	193	13.892
5	3	-5324.4	188.5	13.729
Mean value		-5351.32	241.04	15.258
1	4	-5288.9	284.2	16.858
2	4	-5292	290.5	17.044
3	4	-5294	291.7	17.079	61.44	-22.32	-1.31998642
4	4	-5286.7	280.6	16.751
5	4	-5287.8	282.7	16.814
Mean value		-5289.88	285.94	16.909
1	5	-5267.8	368	19.183
2	5	-5274.2	378.7	19.460
3	5	-5289.3	378.9	19.465	39.12	57.72	3.051219357
4	5	-5266.2	366.5	19.144
5	5	-5156.3	300.4	17.332
Mean value		-5250.76	358.5	18.917
1	6	-5152.8	414.2	20.352
2	6	-5153.5	415.2	20.377
3	6	-5145.6	400.2	20.005	96.84	-96.84	-4.750260842
4	6	-5154.4	416.8	20.416
5	6	-5163.3	431.9	20.782
Mean value		-5153.92	415.66	20.386

LnP(D) likelihood score; SD, standard deviation.

Figure 1. Alleles and their frequencies in Viterbese and Amiata donkey populations for each marker.

Figure 2. Results of population assignment.

Figure 3. Factorial correspondence analysis between Amiata and Viterbese donkeys.

Figure 4. Plot of genomic components estimated for the total sample using the software STRUCTURE from K=2 to K=6. Different colours indicate different clusters.

Figure 5. Results of the analysis of molecular variance.

Table 1. Number of alleles, observed heterozigosity, polymorphism information content, and effective allele number within each microsatellite locus in AD, VD and the total.

Marker	AD				VD				Total
	Na	Hobs	PIC (%)	Ne	Na	Hobs	PIC (%)	Ne	Na	Hobs	PIC (%)	Ne
HMS06	3	0.540	46.64	2.14	2	0.380	30.65	1.61	4	0.676	62.87	3.09
AHT4	10	0.620	67.21	3.32	9	0.797	77.13	4.92	15	0.854	83.79	6.84
HTG7	13	0.840	85.22	7.45	10	0.734	71.77	3.76	13	0.803	78.86	5.08
VHL20	6	0.420	38.08	1.68	5	0.535	49.60	2.15	9	0.504	48.44	2.02
HMS7	6	0.400	38.99	1.69	6	0.432	41.17	1.76	7	0.452	40.82	1.74
HTG10	9	0.580	71.84	3.94	10	0.784	79.04	4.62	10	0.852	83.60	6.75
HMS3	5	0.700	62.99	3.17	6	0.705	66.27	3.39	6	0.786	75.45	4.68
HTG4	3	0.490	43.62	2.00	3	0.310	28.08	1.45	4	0.604	54.44	2.52
HMS2	8	0.640	58.15	2.83	7	0.640	57.62	2.80	10	0.732	69.26	3.73
HTG6	4	0,680	64.80	3.30	4	0.732	68.76	3.74	7	0.737	68.98	3.8
VHL209	3	0.235	19.18	1.27	7	0.391	36.86	1.64	7	0.329	30.72	1.49
HMS45	3	0.580	47.68	2.25	4	0.535	47.76	2.15	4	0.547	48.13	2.21
COR71	7	0.700	67.35	3.45	8	0.674	62.23	3.06	9	0.609	64.62	3.23
COR58	5	0.620	58.67	2.84	7	0.722	67.18	3.60	7	0.708	65.68	3.43
SGV28	4	0.440	43.56	2.14	3	0.541	48.04	2.18	4	0.547	47.62	2.21
ASB23	6	0.785	74.32	4.51	9	0.798	76.77	4.99	9	0.808	78.13	5.21

Na, number of alleles; Hobs, observed heterozigosity; PIC, polymorphism information content; Ne, effective allele number.

Table 2. STRUCTURE: likelihood scores.

K	LnP(D)
2	-5413.04
3	-5351.32
4	-5289.88
5	-5250.76
6	-5153.92

LnP(D), likelihood score.