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

Ray, Nicolas; Currat, Mathias; Foll, Matthieu; Excoffier, Laurent

doi:10.1093/bioinformatics/btq579

Cited by 115 publications

(144 citation statements)

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“…We simulated a range expansion of haploid individuals over a two-dimensional array of demes arranged on a lattice using the software SPLATCHE2 (Ray et al, 2010). Each deme exchanges migrants with its four nearest neighbors as in a two-dimensional stepping stone model (Kimura and Weiss, 1964) with bouncing edges.…”

Section: Methodsmentioning

confidence: 99%

“…Nevertheless, no further analyses were conducted to test this hypothesis. To better characterize the effect of different N values given a fixed Nm on the pattern of genetic diversity as well as to define the influence of N anc , we simulated REs using SPLATCHE2 (Ray et al, 2010). We found that for a fixed Nm: (1) intra-deme genetic diversity depends on N (that is, for increasing N values we found a monotonic increase in the number of haplotypes and in the number of segregating sites) and (2) increasing N leads to a skew in the site frequency spectrum toward an excess of rare variants that leads to more significantly negative values of Tajima's D. We compared these results with an equilibrium stepping stone model: fixing Nm we observed an increase in the genetic diversity for higher N as in the REs but we found no influence on the frequency of rare variants.…”

Section: Introductionmentioning

confidence: 99%

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On the role played by the carrying capacity and the ancestral population size during a range expansion

Mona

2016

Heredity

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Most species are structured and various population genetics models have been proposed to investigate their history. For mathematical tractability, most of these models make the simplifying assumption of equilibrium. Here we focus on the properties of a nonequilibrium spatial explicit model, range expansions (REs). Despite their abundance, many details of their genetic consequences need yet to be fully investigated. The model we studied is characterized by four main parameters: the effective population size of each deme (N), the migration rate per generation per deme (m), the time of the expansion (T exp ) and the effective size of the deme from which the expansion started (N anc ). By means of extensive coalescent simulations, we focused on two aspects of range expansions for fixed Nm: (1) the separate influence of N and m and (2) the role of N anc . We compared our results with an equilibrium stepping stone model and found two main features typical of REs: an excess of rare variants for larger N and a complex interaction between N, T exp and N anc in shaping the degree of population differentiation (which depends only on Nm in the stepping stone model). Finally, we developed an approximate Bayesian computation approach to jointly estimate N and m and to infer N anc . When applied to pseudo-observed data sets, we could correctly recover both N and m (but not N anc ), provided a large number of demes were sampled. These findings highlight how it will be possible to estimate the dispersal rate in nonequilibrium metapopulations by using population genetics approaches.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

On the role played by the carrying capacity and the ancestral population size during a range expansion

Mona

2016

Heredity

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“…We then estimated the fraction of those simulations leading to a Neanderthal introgression level fitting the observations (i.e., between 1.9% and 3.1% of Neanderthal ancestry in contemporary samples). We slightly modified the program SPLATCHE2 (21) to output the number of hybridization events over the whole Neanderthal range and during the whole cohabitation period.…”

Section: Methodsmentioning

confidence: 99%

Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression

Currat

Excoffier

2011

Proc. Natl. Acad. Sci. U.S.A.

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152

113

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Recent studies have revealed that 2-3% of the genome of nonAfricans might come from Neanderthals, suggesting a more complex scenario of modern human evolution than previously anticipated. In this paper, we use a model of admixture during a spatial expansion to study the hybridization of Neanderthals with modern humans during their spread out of Africa. We find that observed low levels of Neanderthal ancestry in Eurasians are compatible with a very low rate of interbreeding (<2%), potentially attributable to a very strong avoidance of interspecific matings, a low fitness of hybrids, or both. These results suggesting the presence of very effective barriers to gene flow between the two species are robust to uncertainties about the exact demography of the Paleolithic populations, and they are also found to be compatible with the observed lack of mtDNA introgression. Our model additionally suggests that similarly low levels of introgression in Europe and Asia may result from distinct admixture events having occurred beyond the Middle East, after the split of Europeans and Asians. This hypothesis could be tested because it predicts that different components of Neanderthal ancestry should be present in Europeans and in Asians.genetic introgression | simulation

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“…This approach is analogous to the approach adopted by ref. 16, but in our model, demographic parameters were linked to primary productivity. We explored a wide range of parameter values, representing scenarios that spanned from climate having no effect on demography (the standard approach used by most population genetics models) to primary productivity having a strong positive effect on population density.…”

mentioning

confidence: 99%

Late Pleistocene climate change and the global expansion of anatomically modern humans

Eriksson¹,

Betti²,

Friend

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

161

164

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The extent to which past climate change has dictated the pattern and timing of the out-of-Africa expansion by anatomically modern humans is currently unclear [Stewart JR, Stringer CB (2012) Science 335:1317-1321. In particular, the incompleteness of the fossil record makes it difficult to quantify the effect of climate. Here, we take a different approach to this problem; rather than relying on the appearance of fossils or archaeological evidence to determine arrival times in different parts of the world, we use patterns of genetic variation in modern human populations to determine the plausibility of past demographic parameters. We develop a spatially explicit model of the expansion of anatomically modern humans and use climate reconstructions over the past 120 ky based on the Hadley Centre global climate model HadCM3 to quantify the possible effects of climate on human demography. The combinations of demographic parameters compatible with the current genetic makeup of worldwide populations indicate a clear effect of climate on past population densities. Our estimates of this effect, based on population genetics, capture the observed relationship between current climate and population density in modern huntergatherers worldwide, providing supporting evidence for the realism of our approach. Furthermore, although we did not use any archaeological and anthropological data to inform the model, the arrival times in different continents predicted by our model are also broadly consistent with the fossil and archaeological records. Our framework provides the most accurate spatiotemporal reconstruction of human demographic history available at present and will allow for a greater integration of genetic and archaeological evidence.human dispersals | colonization | population bottlenecks | net primary productivity | most recent common ancestor

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

Abstract: mathias.currat@unige.ch

Cited by 115 publications

References 20 publications

On the role played by the carrying capacity and the ancestral population size during a range expansion

On the role played by the carrying capacity and the ancestral population size during a range expansion

Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression

Late Pleistocene climate change and the global expansion of anatomically modern humans

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