scholarly journals Investigating population continuity with ancient DNA under a spatially explicit simulation framework

BMC Genetics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Nuno Miguel Silva ◽  
Jeremy Rio ◽  
Mathias Currat
2018 ◽  
Vol 11 (9) ◽  
pp. 1642-1655 ◽  
Author(s):  
Nuno Miguel Silva ◽  
Jeremy Rio ◽  
Susanne Kreutzer ◽  
Christina Papageorgopoulou ◽  
Mathias Currat

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

2016 ◽  
Author(s):  
NM Silva ◽  
S Kreutzer ◽  
C Papageorgopoulou ◽  
M Currat

AbstractRecent advances in sequencing techniques provide means to access direct genetic snapshots from the past with ancient DNA data (aDNA) from diverse periods of human prehistory. Comparing samples taken in the same region but at different time periods may indicate if there is continuity in the peopling history of that area or if a large genetic input, such as an immigration wave, has occurred. Here we propose a new modeling approach for investigating population continuity using aDNA, including two fundamental elements in human evolution that were absent from previous methods: population structure and migration. The method also considers the extensive temporal and geographic heterogeneity commonly found in aDNA datasets. We compare our spatially-explicit approach to the previous non-spatial method and show that it is more conservative and thus suitable for testing population continuity, especially when small, isolated populations, such as prehistoric ones, are considered. Moreover, our approach also allows investigating partial population continuity and we apply it to a real dataset of ancient mitochondrial DNA. We estimate that 91% of the current genetic pool in central Europe entered the area with immigrant Neolithic farmers, but a genetic contribution of local hunter-gatherers as large as 83% cannot be entirely ruled out.


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.


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