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mec12294-sup-0001-TableS1-S5.pdfapplication/PDF219K

Table S1 Characteristics of the ecological zones of the study area and the respective gene pools observed in each eco-zone.

Table S2 Characteristics of the thirty ISAG/FAO recommended microsatellite markers used in the current study.

Table S3 Number of alleles shared between the three gene pools observed in the current study.

Table S4a Total number of gene pool specific alleles observed from the analysis of thirty microsatellite markers in 15 chicken populations.

Table S4b Gene pool specific alleles and their frequencies.

Table S5 Measures of allelic and genetic diversity for each population after excluding individuals with less than 90% of their genotype proportion from each gene pool.

mec12294-sup-0002-FigS1-S8.pdfapplication/PDF992K

Fig. S1 Bayesian analysis of population structure in East African village chickens based on 30 microsatellite loci for three of the four models (1, 2 and 4, see materials and methods) tested in the current study.

Fig. S2 Estimated number of populations (K) from the program STRUCTURE for East African village chickens.

Fig. S3 Bayesian analysis of population structure in East African village chickens.

Fig. S4 Distribution across loci of variance (Var), similarity (Cos2) and typological (Cov2) values for each marker for the components of the first and second axes in percentages (a and b).

Fig. S5 a) Bayesian analysis of population structure in East African village chickens after including four breeds of commercial chickens.

Fig. S6 Regression analysis between geographic distance (Km) from Mombasa at the Kenya Coast to the hinterland of Uganda with the proportion (%) of gene pools II and III in the two countries.

Fig. S7 FST values from 30 microsatellite loci for the three gene pools observed in East Africa plotted against (a) expected heterozygosity as obtained from Lositan and (b) against log10(q-value) generated using BayeScan.

Fig. S8 Spatial geographic distribution pattern of mtDNA haplogroups and the three microsatellite gene pools observed among village chickens from the East African region

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