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In Lossi, the post epidemic sample differed both in sex ratio and group composition from the pre-epidemic sample: the post-epidemic sample contained proportionally more males and more solitary individuals than the pre-epidemic sample (Table 1).
Comparison between pre and post-epidemic sample for each population was achieved by resampling (999 times) randomly the relevant half matrices, calculating the difference between the means of the pre and post epidemic sample and testing if its distribution was centered on 0 (as expected if relatedness did not differ between the two samples, see [79]).
The EV71 isolate Fuyang573 (subgenotype C4a, GenBank accession number: HM064456, isolated from a 2008 epidemic sample in Anhui province) was used throughout this study, unless otherwise stated.
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We tested difference in sex ratio between pre and post epidemic samples using χ2 tests.
In the early epidemic, samples of culled flocks were not tested during massive culling.
Similarly the epidemic samples were also collected from insects representing the same life stages at the time of collection from each aggressive patch.
We computed for individuals sampled after the epizooties their Lhome within the post-epidemic sample and within the pre-epidemic sample.
In fact, analysis of sex-ratio and group composition of Lossi samples revealed that the post-epidemic sample contains a higher proportion of males and of solitary individuals than in the pre-epidemic sample.
We then compared the distribution of Lhome frequencies within pre-epidemic sample and within post-epidemic sample with a χ2 test, in order to test if distribution of Lhome within pre-epidemic was skewed toward low value of Lhome.
Indeed, the Lossi post-epidemic sample encompassed only two social groups whereas the Lokoué post-epidemic sample gathered individuals from 8 different social groups thanks to the higher remnant population size after outbreak in this population.
By contrast, in this population, the group composition differed between the two samples since only social groups were sampled in the pre-epidemic sample whereas 33% of genotyped individuals in the post-epidemic sample were solitary individuals.
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