Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum

Tellier, Aurélien; Pfaffelhuber, Peter; Haubold, Bernhard; Naduvilezhath, Lisha; Rose, Laura; Städler, Thomas; Stephan, Wolfgang; Metzler, Dirk

doi:10.1371/journal.pone.0018155

Cited by 18 publications

(30 citation statements)

References 36 publications

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“…However, in our case, these more sophisticated models have the property of having divergence time and specific migration rates as free parameters for several pairs of populations. A recent simulation study showed that the joint estimation of these two parameters in an ABC framework does not yield satisfying results (Tellier et al 2011). Indeed, it is not clear at the present time which summarization of the raw data set would allow for an accurate joint estimation of divergence times and migration rates within an ABC framework.…”

Section: Discussionmentioning

confidence: 92%

Demographic Inference Reveals African and European Admixture in the North AmericanDrosophila melanogasterPopulation

et al. 2013

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Drosophila melanogaster spread from sub-Saharan Africa to the rest of the world colonizing new environments. Here, we modeled the joint demography of African (Zimbabwe), European (The Netherlands), and North American (North Carolina) populations using an approximate Bayesian computation (ABC) approach. By testing different models (including scenarios with continuous migration), we found that admixture between Africa and Europe most likely generated the North American population, with an estimated proportion of African ancestry of 15%. We also revisited the demography of the ancestral population (Africa) and found-in contrast to previous work-that a bottleneck fits the history of the population of Zimbabwe better than expansion. Finally, we compared the site-frequency spectrum of the ancestral population to analytical predictions under the estimated bottleneck model. TO date, several studies have confirmed that Drosophila melanogaster originated in sub-Saharan Africa and spread to the rest of the world (Lachaise et al. 1988;David and Capy 1988;Begun and Aquadro 1993; Andolfatto 2001;Stephan and Li 2007). With its cosmopolitan distribution we expect that different populations have evolved and adapted differently to distinct environments, making D. melanogaster a perfect study system for both adaptation and population history. Extensive research has been performed to detect signatures of adaptation at the genome level (Sabeti et al. 2006;Li and Stephan 2006;Zayed and Whitfield 2008). Such detection usually depends on the underlying demographic scenario, since demographic events can leave similar patterns on the genome as adaptive (selective) events (Kim and Stephan 2002;Glinka et al. 2003;Jensen et al. 2005;Nielsen et al. 2005;Pavlidis et al. 2008Pavlidis et al. , 2010a. Therefore, a better understanding of the demography of a population will not only allow us to estimate past and present population sizes and the times of the population size changes but will also decrease the rate of false positives of signatures of adaptation. Here we study the demography of African, European, and North American populations, with an emphasis on the North American population.There is evidence that D. melanogaster colonized North America ,200 years ago (Johnson 1913;Sturtevant 1920;Keller 2007). D. melanogaster (then known as D. ampelophila) was first reported in New York in 1875 by New York State entomologist Lintner (Lintner 1882;Keller 2007). In the year 1879 several articles were published indicating the appearance of D. melanogaster in several parts of eastern North America, including Connecticut and Massachusetts (Johnson 1913). At that time the dipteran fauna was very well described. It is therefore unlikely that entomologists would have overlooked D. melanogaster for long (Keller 2007). Less than 25 years after its introduction, D. melanogaster became the most common dipteran species in North America (Howard 1900). Johnson (1913) suggested that North America could have been colonized from the tropics, since the fir...

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Section: Discussionmentioning

confidence: 92%

Demographic Inference Reveals African and European Admixture in the North AmericanDrosophila melanogasterPopulation

et al. 2013

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“…A simulation study to compare a variant of Jaatha with MIMAR (Becquet & Przeworski 2007) and PopABC (Lopes et al. 2009) has been performed by Tellier et al. (2011).…”

Section: Methods and Modelsmentioning

confidence: 99%

“…Li & Stephan (2006) showed that it is worthwhile to use more information from the JSFS than these four summary statistics for inference of demographic histories using population genetic data. Other JSFS‐based sets of summary statistics are examined by Tellier et al. (2011), with the main conclusion that especially further division of the shared polymorphisms results in better estimations of divergence times and migration rates.…”

Section: Introductionmentioning

confidence: 99%

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Jaatha: a fast composite-likelihood approach to estimate demographic parameters

2011

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While information about a species' demography is interesting in its own right, it is an absolute necessity for certain types of population genetic analyses. The most widely used methods to infer a species' demographic history do not take intralocus recombination or recent divergence into account, and some methods take several weeks to converge. Here, we present Jaatha, a new composite-likelihood method that does incorporate recent divergence and is also applicable when intralocus recombination rates are high. This new method estimates four demographic parameters. The accuracy of Jaatha is comparable to that of other currently available methods, although it is superior under certain conditions, especially when divergence is very recent. As a proof of concept, we apply this new method to estimate demographic parameters for two closely related wild tomato species, Solanum chilense and S. peruvianum. Our results indicate that these species likely diverged 1.44·N generations ago, where N is the effective population size of S. chilense, and that some introgression between these species continued after the divergence process initiated. Furthermore, S. peruvianum likely experienced a population expansion following speciation.

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“…There are no sufficient summary statistics at hand, but for the IM model the joint site frequency spectrum (JSFS) between the two populations was reported to be a particularly informative summary statistic (Tellier et al, 2011). However, for N samples in each of the two demes, the JSFS has (N + 1) 2 − 2 entries, so even for small datasets it is very high-dimensional.…”

Section: The Evolutionary History Of Bornean and Sumatran Orang-utansmentioning

confidence: 99%

Approximate maximum likelihood estimation for population genetic inference

Bertl

Ewing

Kosiol

et al. 2017

Statistical Applications in Genetics and Molecular Biology

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Abstract:In many population genetic problems, parameter estimation is obstructed by an intractable likelihood function. Therefore, approximate estimation methods have been developed, and with growing computational power, sampling-based methods became popular. However, these methods such as Approximate Bayesian Computation (ABC) can be inefficient in high-dimensional problems. This led to the development of more sophisticated iterative estimation methods like particle filters. Here, we propose an alternative approach that is based on stochastic approximation. By moving along a simulated gradient or ascent direction, the algorithm produces a sequence of estimates that eventually converges to the maximum likelihood estimate, given a set of observed summary statistics. This strategy does not sample much from low-likelihood regions of the parameter space, and is fast, even when many summary statistics are involved. We put considerable efforts into providing tuning guidelines that improve the robustness and lead to good performance on problems with high-dimensional summary statistics and a low signal-to-noise ratio. We then investigate the performance of our resulting approach and study its properties in simulations. Finally, we re-estimate parameters describing the demographic history of Bornean and Sumatran orang-utans.

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Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum

Cited by 18 publications

References 36 publications

Demographic Inference Reveals African and European Admixture in the North AmericanDrosophila melanogasterPopulation

Demographic Inference Reveals African and European Admixture in the North AmericanDrosophila melanogasterPopulation

Jaatha: a fast composite-likelihood approach to estimate demographic parameters

Approximate maximum likelihood estimation for population genetic inference

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