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SCALETOOL IntroductionDriversBiodiversityPolicies and managementConnectivity and protected areas
From species traits to dispersal distances Simulation of genetic data Population Viability Sex-biased dispersal Biodiversity scaling Perspectives for landscape scale management Conservation strategies at appropriate spatial scales
 

Spatially explicit simulation of genetic data with SPLATCHE 2 Methods and Applications

Genetic variability at different scales is an important component of biodiversity. Under slow range contraction species lose more diversity than under fast contraction and the loss of diversity due to fragmentation accelerates across scales.
Computer simulations can mimic real-world processes and allow us to study which aspects of ecology and land-use might affect species genetic diversity. We have developed the program SPLATCHE 2 (Ray et al. 2010), which performs spatially explicit simulations of genetic processes under different environmental scenarios and accounting for recombination, complex migration and long-distance dispersal. First, SPLATCHE 2 performs a demographic simulation over a map (Figure A). Second, the evolutionary history of user-specified samples can be recovered through the coalescent genealogy (Figure B). Finally, genetic data (i.e. DNA, STRs and SNPs) can be obtained by simulating molecular evolution along the coalescent genealogy (Figure B). Although the model makes several assumptions (such as the constancy of a molecular clock and that generations are non-overlapping) it is probably one of the most realistic pieces of software available for its purpose. SPLATCHE 2 may thus be used to predict genetic diversity under complex demographic scenarios and could thus be useful for many projects studying genetic diversity in spatially explicit and dynamic environments (see Arenas et al. in press).

We have used SPLATCHE 2 to study:
  1. the effect of increasing barriers to gene flow at different spatial scales. We found that strong levels of fragmentation result in a severe loss of genetic diversity in the population at a global scale and that the detection of this decreased diversity requires sampling at different scales (Mona et al. 2014).
  2. the effect of range contractions on genetic diversity. We found that fast contractions preserve higher levels of diversity and induce lower levels of genetic differentiation among refuge areas than slow contractions towards refuge areas. Thus slow contractions have the highest negative impact on final levels of diversity (Arenas et al. 2012).
  3. the effective levels of fragmentation of a species, derived from genetic data gathered at different scales over the species' range. We found that the degree of environmental heterogeneity can be very well estimated but only if all other parameters of the model are known.

Schematic representation of the methods implemented in SPLATCHE 2 to simulate genetic data. A) Snapshots of SPLATCHE 2 to simulate a human colonization of Europe (range expansion) from the Middle East. Further details can be found in (Arenas et al. 2014). B) Illustrative example of sampling and reconstruction of the samples' genealogy. Circles indicate sampling places. Then, a coalescent simulation (backwards in time) is performed to get a genealogy of the samples compatible with past demography. Finally, a molecular evolution simulation is performed forwards in time from a sequence assigned to the root node. An illustrative example of this procedure is included by using 3 nucleotides, where circles include the sequence for each node and each substitution event is represented by a number (sequence position) followed by the ancestral and derived states involved in the substitution.

References

Arenas, M., Francois, O., Currat, M., Ray, N. and Excoffier, L. (2013). Influence of admixture and paleolithic range contractions on current European diversity gradients. Mol Biol Evol, 30, 57-61.

Arenas, M., Mona, S., Trochet, A., Sramkova Hanulova, A., Currat, M., Ray, N., Chikhi, L., Rasteiro, R., Schmeller, D.S. and Excoffier, L. (2014). The scaling of genetic diversity in a changing and fragmented world, pp. 55-60. In: HENLE, K., S.G. POTTS, W.E. KUNIN, Y.G. MATSINOS, J. SIMILĂ„, J.D. PANTIS, V. GROBELNIK, L. PENEV & S. SETTELE (eds.): Scaling in Ecology and Biodiversity Conservation. Pensoft Publishers, Sofia.

Arenas, M., Ray, N., Currat, M. and Excoffier, L. (2012). Consequences of Range Contractions and Range Shifts on Molecular Diversity. Mol Biol Evol, 29, 207-218.

Mona, S., Ray, N., Arenas, M. and Excoffier, L. (2014). Genetic consequences of habitat fragmentation during a range expansion. Heredity, 112, 291-299.

Ray, N., Currat, M., Foll, M. and Excoffier, L. (2010). SPLATCHE 2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics, 26, 2993-4.
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