Additional file 1:

Table showing giraffe sampling localities and sample sizes for mtDNA characterization with resulting mtDNA control region haplotypes

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Additional file 2:

Figure showing maximum parsimony phylogeny of giraffe (Giraffa camelopardalis) mtDNA haplotypes, rooted with okapi (Okapia johnstoni)

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Additional file 3:

Figure showing maximum parsimony phylogeny of giraffe (Giraffa camelopardalis) mtDNA haplotypes, rooted using midpoint rooting

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Additional file 4:

Figure showing minimum evolution phylogeny of giraffe (Giraffa camelopardalis) mtDNA haplotypes, rooted with okapi (Okapia johnstoni)

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Additional file 5:

Figure showing minimum evolution phylogeny of giraffe (Giraffa camelopardalis) mtDNA haplotypes, rooted using midpoint rooting

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Additional file 6:

Figure showing maximum likelihood phylogeny of giraffe (Giraffa camelopardalis) mtDNA haplotypes, rooted with okapi (Okapia johnstoni)

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Additional file 7:

Figure showing maximum likelihood phylogeny of giraffe (Giraffa camelopardalis) mtDNA haplotypes, rooted using midpoint rooting

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Additional file 8:

Table of AMOVA results according to subspecific groupings

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Additional file 9:

Table of sample sizes, number of mitochondrial haplotypes and molecular diversity indices per sampling locality and subspecies

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Additional file 10:

Table of sampling locations (six historical subspecies, 30 sample sites, 381 individuals) for microsatellite characterization

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Additional file 11:

Table of summary statistics for microsatellite data (381 specimens, all populations and pelage subspecies)

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Additional file 12:

Tables showing (A) observed and expected heterozygosity, and deviations from Hardy-Weinberg equilibrium in six giraffe subspecific populations, and (B) observed and expected heterozygosity, and deviations from Hardy-Weinberg equilibrium in 16 giraffe populations

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Additional file 13:

Tables showing (A) posterior probability population assignments of 381 Individuals, based on assignment to pelage/subspecies designations using STRUCTURE [19], and (B) subspecies assignment of 381 individuals, based on assignment to pelage/subspecies designations, using multilocus genotypes and Bayesian analysis (Rannala and Mountain method in Geneclass2 [46,47])

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Additional file 14:

Table of STRUCTURE [23] cluster results identify three possible subspecies hybrids, four population hybrids within the same subspecies and one possible population migrant within the same subspecies

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Additional file 15:

Figure showing STRUCTURE [19] cluster assignments of detected giraffe hybrids

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Additional file 16:

Tables showing (A) pairwise F_st values and statistical significance for the six giraffe subspecies; (B) pairwise values for Nei's genetic distance among six giraffe subspecies; (C) G.c. angolensis (Angolan) population pairwise comparison Fst values and statistical significance; (D) G.c. reticulata (Reticulated) population pairwise comparison Fst values and statistical significance; (E) G.c. rothschildi (Rothschild's) population pairwise comparison Fst values and statistical significance; (F) G.c. tippelskirchi (Masai) population pairwise comparison Fst values and statistical significance; and (G) G.c. tippelskirchi (Masai) Serengeti N.P. population pairwise comparison Fst values and statistical significance

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Additional file 17:

Table showing migration rates among giraffe subspecies

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Additional file 18:

Table of primer sequences and amplification characteristics of Giraffa camelopardalis microsatellite locus NECK484

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Additional file 19:

Figure showing likelihood values for inferred number of genetic clusters (K) from STRUCTURE [23] (three iterations per value of K)

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Additional file 20:

Table of overall F_is values per subspecies, and per population

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Additional file 21:

Table of Mantel test of isolation by distance results (correlation of genetic distance (Fst/(1-Fst) with geographic distance)

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Additional file 22:

Table of AMOVA using microsatellite data results

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