SteepSelection_CDPOP

3) Steep spatial selection gradient (‘steep’): For this scenario, stronger spatial selection gradients were assigned to each genotype, with the relative fitness coefficients for AA of 1.0, 0.6, and 0.2 for black, mixed, and white waters, respectively. An opposite spatial selection gradient was implemented for aa (0.2, 0.6, and 1.0 for black, mixed, and white waters, respectively). Aa received a uniform selection gradient of 0.2 in all three scenarios

Conceptual models for the cross-infection dynamics between (a) a single host-vector system, which includes <i>j—</i>1 relapses between <i>j</i> infected compartments and (b) a coupled host-vector system with no relapses in either host.

<p>Dashed lines are vital rates for each population, where solid lines refer to interaction rates between compartments. See <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004428#pntd.0004428.t001" target="_blank">Table 1</a> for a summary of notation.</p

Parameter values in the TBRF model for <i>j-1</i> relapses between <i>j</i> infected compartments (rates are per month, competency values are probabilities per bite).

<p>The subscripts <i>ps</i> and <i>dm</i> denote values used in the pine squirrel and deer mouse host-vector system, respectively. Note that if the subscripts do not appear, then the parameter is the same value in both systems.</p

Parameters and variable notation in the host-vector TBRF model for <i>j—</i>1 relapses between <i>j</i> infected compartments (rates are per month, competency values are probabilities (per bite)) and dimensionless forms (rescaled by γ or normalized by <i>N</i>(0)).

<p>In the coupled system, additional subscripts with <i>ps</i> represent the pine squirrel host-vector system and <i>dm</i> represents the deer mouse host-vector system.</p

GentleSelection_CDPOP

2) Gentle spatial selection gradient (‘gentle’): Here, we used a ‘gentle’ spatial selection gradient corresponding to the three river color locations. For AA, we used the relative fitness coefficients of 0.4, 0.3, and 0.2 for black, mixed, and white waters, respectively. For Aa, we implemented an opposite spatial selection gradient (relative fitness coefficients of 0.2, 0.3, and 0.4 for black, mixed, and white waters, respectively)

Single host-vector system.

<p>Increasing number of infected compartments are added to the single host-vector system and <i>R</i>_<i>0</i> is plotted (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004428#pntd.0004428.e006" target="_blank">Eq 5</a>). <i>R</i>_<i>0</i> becomes greater than one at four relapses.</p

AFLP data

AFLP data for Steatogenys elegans cryptic species 1 and 2 including sampling locations

BarrierRemove_HighMigration_CDPOP

Simulating Secondary Contact 1) We initially placed complete barriers on the riverscape to restrict movement of individuals to and from the three subgroups (Negro, Maderia, and Amazon). We then conducted an isolation-by-riverine distance simulation modeling experiment within each subgroup using a movement distance that considered the maximum extent of the riverscape (i.e., mimicking the spatial selection simulation parameters or high migration)

Coupled host-vector system.

<p>An incompetent deer mouse (<i>Peromyscus maniculatus</i>) host system (<i>c</i>_<i>dm</i> = 0.2) is coupled with a competent pine squirrel (<i>Tamiasciurus hudsonicus</i>) host system (<i>c</i>_<i>ps</i> = 0.9). <i>R</i>_<i>0</i> is plotted (Eqs <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004428#pntd.0004428.e013" target="_blank">9</a> and <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004428#pntd.0004428.e014" target="_blank">10</a>) for the deer mouse host system that contained no relapses and the pine squirrel host system with increasing number of infected compartments. <i>R</i>_<i>0</i> becomes greater than one at seven relapses. </p

Simulation data

The final generation (generation 1250) of each simulation run and replicate. Simulations are divided into no selection simulations ("Nsims"), gradient selection simulations ("Gsims"), and discrete selection simulations ("H1/H5/H9sims")