Mortality ascertainment was by "exact matches", i.e., sharing locality, demographic factors and period of care, with subject record between the SSA Death Master File database and our Texas tuberculosis file, using previously described methods [ 6].
For example, lineage A2 was characterised by six alleles that were shared between localities while the remaining alleles were locality specific.
Six alleles were shared between localities and the presence of several unique alleles within localities may reflect evolutionarily old populations, which may have served as core regions for colonisation.
Although the populations were significantly differentiated in allele frequencies, the overwhelming majority of polymorphic positions were shared among localities, and fixed differences were not observed between the localities (Table 4).
While between Dzanga Sangha (n = 54; 11 unique haplotypes) and Lope (n = 17; six unique haplotypes), only one haplotype was shared between localities.
Thirty-two unique mtDNA haplotypes were found among the 47 samples of P. reddelli sequenced, none of which were shared among localities.
Thirty-two of the 86 phased ITS alleles were unique and twelve were not shared among localities (Austin, 4; San Antonio, 3; New Braunfels, 2; and Junction, Mountain Home, and Camp Wood, 1 each).
Between the highly sampled southern African locations of Kruger (n = 50 elephants; nine unique haplotypes) and northern Namibia (n = 60; nine unique haplotypes), no haplotypes were shared between localities.
Third, while increasing the sample size of the voucher collection might increase the number of haplotypes found to be shared between localities, the larger sampling would also tend to identify rare haplotypes.
Within another Trust three generic locality teams covering the same locality shared one protocol (3); an in-patient unit covering this locality and other areas used two protocols (3 and 5); and a specilaist adolescent team covering used another protocol (protocol 4).
