scholarly journals SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination

2010 ◽  
Vol 26 (23) ◽  
pp. 2993-2994 ◽  
Author(s):  
Nicolas Ray ◽  
Mathias Currat ◽  
Matthieu Foll ◽  
Laurent Excoffier
2008 ◽  
Author(s):  
Carlos Gustavo Tornquist ◽  
Joao Mielnickzuk ◽  
Philip Walter Gassman

2017 ◽  
Author(s):  
Jacob Thomas ◽  
Samit S. Watve ◽  
William C. Ratcliff ◽  
Brian K. Hammer

AbstractHorizontal gene transfer can have profound effects on bacterial evolution by allowing individuals to rapidly acquire adaptive traits that shape their strategies for competition. One strategy for intermicrobial antagonism often used by Proteobacteria is the genetically-encoded contact-dependent Type VI secretion system (T6SS); a weapon used to kill heteroclonal neighbors by direct injection of toxic effectors. Here, we experimentally demonstrate thatVibrio choleraecan acquire new T6SS effector genes via horizontal transfer and utilize them to kill neighboring cells. Replacement of one or more parental alleles with novel effectors allows the recombinant strain to dramatically outcompete its parent. Through spatially-explicit simulation modeling, we show that the HGT is risky: transformation brings a cell into conflict with its former clonemates, but can be adaptive when superior T6SS alleles are acquired. More generally, we find that these costs and benefits are not symmetric, and that high rates of HGT can act as hedge against competitors with unpredictable T6SS efficacy. We conclude that antagonism and horizontal transfer drive successive rounds of weapons-optimization and selective sweeps, dynamically shaping the composition of microbial communities.


2017 ◽  
Vol 74 (6) ◽  
pp. 894-906 ◽  
Author(s):  
Abbey E. Camaclang ◽  
Janelle M.R. Curtis ◽  
Ilona Naujokaitis-Lewis ◽  
Mark S. Poesch ◽  
Marten A. Koops

We developed a spatially explicit simulation model of poaching behaviour to quantify the relative influence of the intensity, frequency, and spatial distribution of poaching on metapopulation viability. We integrated our model of poaching with a stochastic, habitat-based, spatially explicit population model, applied it to examine the impact of poaching on northern abalone (Haliotis kamtschatkana) metapopulation dynamics in Barkley Sound, British Columbia, Canada, and quantified model sensitivity to input parameters. While demographic parameters remained important in predicting extinction probabilities for northern abalone, our simulations indicate that the odds of extinction are twice as high when populations are subjected to poaching. Viability was influenced by poaching variables that affect the total number of individuals removed. Of these, poaching mortality was the most influential in predicting metapopulation viability, with each 0.1 increase in mortality rate resulting in 22.6% increase in the odds of extinction. By contrast, the location and spatial correlation of events were less important predictors of viability. When data are limited, simulation models of poaching combined with sensitivity analyses can be useful in informing management strategies and future research directions.


Behaviour ◽  
2016 ◽  
Vol 153 (9-11) ◽  
pp. 1247-1266 ◽  
Author(s):  
T. Czárán ◽  
Duur K. Aanen

The evolution of cooperation is difficult to understand, because cheaters — individuals who profit without cooperating themselves — have a benefit in interaction with cooperators. Cooperation among humans is even more difficult to understand, because cooperation occurs in large groups, making cheating a bigger threat. Restricting cooperation to members of one’s own group based on some tag-based recognition of non-group members (allorecognition) has been shown to stabilise cooperation. We address how spatial structure and group size affect the opportunities for cheating such tag-based cooperation in a spatially explicit simulation. We show that increased group diversity, under conditions of limited dispersal, reduces the selective opportunities for cheaters. A small number can already be sufficient to keep cheating at a low frequency. We discuss how marginal additional benefits of increased group size, above the benefits of local cooperation, can provide the selective pressure to reduce the number of group identities and discuss possible examples.


2008 ◽  
Vol 13 (3) ◽  
pp. 395-414 ◽  
Author(s):  
ERWIN H. BULTE ◽  
RANDALL B. BOONE ◽  
RANDY STRINGER ◽  
PHILIP K. THORNTON

ABSTRACTTraditional grazing grounds near Amboseli National Park (Kenya) are being rapidly converted to cropland – a process that closes important wildlife corridors. We use a spatially explicit simulation model that integrates ecosystem dynamics and pastoral decision-making to explore the scope for introducing a ‘payments for ecosystem services’ scheme to compensate pastoralists for spillover benefits associated with forms of land use that are compatible with wildlife conservation. Our break-even cost analysis suggests that the benefits of such a scheme likely exceed its costs for a large part of the study area, but that ‘leakage effects’ through excessive stocking rates warrant close scrutiny.


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