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    Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012.
    (2017-06) Bloomfield SJ; Benschop J; Biggs PJ; Marshall JC; Hayman DTS; Carter PE; Midwinter AC; Mather AE; French NP
    During 1998-2012, an extended outbreak of Salmonella enterica serovar Typhimurium definitive type 160 (DT160) affected >3,000 humans and killed wild birds in New Zealand. However, the relationship between DT160 within these 2 host groups and the origin of the outbreak are unknown. Whole-genome sequencing was used to compare 109 Salmonella Typhimurium DT160 isolates from sources throughout New Zealand. We provide evidence that DT160 was introduced into New Zealand around 1997 and rapidly propagated throughout the country, becoming more genetically diverse over time. The genetic heterogeneity was evenly distributed across multiple predicted functional protein groups, and we found no evidence of host group differentiation between isolates collected from human, poultry, bovid, and wild bird sources, indicating ongoing transmission between these host groups. Our findings demonstrate how a comparative genomic approach can be used to gain insight into outbreaks, disease transmission, and the evolution of a multihost pathogen after a probable point-source introduction.
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    Can survival analyses detect hunting pressure in a highly connected species? Lessons from straw-coloured fruit bats.
    (2016-08) Hayman DTS; Peel AJ
    Animal behaviour, social structure and population dynamics affect community structure, interspecific interactions, and a species' resilience to harvesting. Building on new life history information for the straw-coloured fruit bat (Eidolon helvum) from multiple localities across Africa, we used survival analyses based on tooth-cementum annuli data to test alternative hypotheses relating to hunting pressure, demography and population connectivity. The estimated annual survival probability across Africa was high (≥ 0.64), but was greatest in colonies with the highest proportion of males. This difference in sex survival, along with age and sex capture biases and out-of-phase breeding across the species' distribution, leads us to hypothesize that E. helvum has a complex social structure. We found no evidence for additive mortality in heavily hunted populations, with most colonies having high survival with constant risk of mortality despite different hunting pressure. Given E. helvum's slow life history strategy, similar survival patterns and rate among colonies suggest that local movement and regional migration may compensate for local excess hunting, but these were also not clearly detected. Our study suggests that spatio-temporal data are necessary to appropriately assess the population dynamics and conservation status of this and other species with similar traits.