Fig. 2: Infection time distributions from our transmission
network model for individuals involved in a putative transmission chain,
along with the likely direction of transmission (red arrows) and the
spatial context (see Fig. S5/S6 for information on other transmission
events in the treatment and stable region). Grey circles encompassing
puma silhouettes in the map insets represent known territorial overlap
between individuals (based on observations from K. Logan) and is not
representative of home range size. Orange: lag 1 period from the start
of the no-hunting period when males are recruited to the study area and
lag 2 period at the start of the hunting period until the population
declines, light yellow: hunting pressure relieved, red: hunting
pressure. Birth year is indicated by the cub silhouette, and death year
of M73 is indicated by the black horizontal line. The orange horizontal
line indicates when the FIVpco CO III lineage was
introduced into this population based on node estimates from
(Fountain-Jones et al. 2019). Red horizontal lines indicate
transmission time distributions (overlap between infection time
distributions) and ‘trans’ means ‘likely transmitted to’.
Fig. 3. Eliminating hunting mortality led to: (a) overall
greater phylogenetic clustering (i.e., lower phylogenetic diversity) of
FIVpco isolates standardized for sample number and (b)
an increase in FIVpco population growth rate that was
(c) strongly correlated with male population size rather than (d) female
population size. (a) Standardized phylogenetic diversity (*: SES.PD,
standardized effect size phylogenetic diversity calculated from 1000
posterior trees) estimates revealed strong patterns of phylogenetic
clustering (smaller distances between isolates than expected by chance)
when hunting pressure was relieved (negative values of SES.PD).
Otherwise, FIVpco isolates were more dispersed across
the tree (SES. PD ~ 0, indicated by the dashed line).
Estimates of FIVpco prevalence (number of qPCR
positives/total number sampled) are provided next to each box and
whisker plot with number of individuals tested shown in parentheses (see
Fig. S8 for estimates of prevalence across years). (b) Viral population
growth rate was estimated using Bayesian phylodynamic reconstruction
(Volz & Didelot 2018). See Fig. S7a for the corresponding skyline plot
(effective population size through time estimated via thephylodyn model (Karcher et al. 2016)) for the treatment
region and Fig. S7b/c for complementary plots for the
FIVpco clade dominant in the stable region. Lg refers to
the period between hunting being reinstated and the start of population
decline.