Study population
Our study population consisted of 519 koalas that were monitored between 2013 and 2017 as part of a management program associated with a 13km rail infrastructure project in Moreton Bay Council, Queensland, Australia (area centroid: -27.234°; 153.036°), and described in detail in . During the five-year program, most of the population (>95% of individuals in the study area) was intensively monitored. Individuals were first captured between 13/03/2013 and 02/02/2017 using either live traps or flagging pole methods, and were fitted with VHF collars. After their first capture, individuals were then periodically re-caught at least every six months for routine veterinary exams, or earlier if they were observed with visible signs of disease (see below) or injury. Tissue samples were taken and ear tags fitted at first capture, and blood samples were taken during routine veterinary examinations, at first capture and at subsequent check-ups. Blood samples were stored at -20°C, and tissue samples were stored in 70% ethanol. Individuals were given a comprehensive veterinary examination each time they were caught, which included recording of sex, age, and presence of a joey (offspring) for females (either through the female having a back-riding or pouch joey or an elongated teat, or through a pregnancy observed by sonogram). Ageing of koalas relied on examination of their tooth wear . They were then tested for the presence of chlamydia bacterium and inspected for visible signs of chlamydial disease (see below for full details). During the project, individuals were treated for any illness (including chlamydial disease, see below) or injury, and some individuals were also included in a chlamydia vaccination trial, which involved a subset of individuals being vaccinated for chlamydia at their first capture (see ). VHF tracking of individuals took place approximately twice a week. By identifying the time of the year in which joeys were born, and accounting for the gestation period (one month), based on the birth of 350 joeys between 2013 and 2016, we determined the breeding season to occur from September to December in this population. The analyses presented here used data from those individuals for which we had complete genetic, spatial and disease status data (described below), a total of N = 342. The dataset included some joeys (N = 4), because dependent joeys have been found to be infected by chlamydia as young as nine months old (Nyari et al. 2017) and the youngest dependent joey sampled in this survey was 10 months old.
The monitoring program was conducted under animal ethics approvals (Queensland Department of Agriculture and Fisheries CA 2012/03/597, CA 2013/09/719, CA 2014/06/777, CA 2015/03/852, and CA 2016/03/950) and scientific purposes permits (Queensland Department of Environment and Heritage Protection WISP 11525212, WISP 16125415, WISP 13661313, WITK 14173714 and WISP 17273716).