scholarly journals Testing Hypotheses of Diversification in Panamanian Frogs and Freshwater Fishes Using Hierarchical Approximate Bayesian Computation with Model Averaging

Diversity ◽  
2018 ◽  
Vol 10 (4) ◽  
pp. 120 ◽  
Author(s):  
Justin Bagley ◽  
Michael Hickerson ◽  
Jerald Johnson
Keyword(s):  
Freshwater Fish ◽  
Dna Sequences ◽  
Approximate Bayesian Computation ◽  
Bayes Factor ◽  
Fish Assemblages ◽  
Model Averaging ◽  
External Information ◽  
Bayesian Computation ◽  
Genetic Structuring ◽  
Approximate Bayesian

Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Molecular Ecology 1998, 7, 499–517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels.

scholarly journals Testing hypotheses of diversification in Panamanian frogs and freshwater fishes using hierarchical approximate Bayesian computation with model averaging

2018 ◽  
Author(s):  
Justin C Bagley ◽  
Michael J Hickerson ◽  
Jerald B Johnson
Keyword(s):  
Freshwater Fish ◽  
Dna Sequences ◽  
Approximate Bayesian Computation ◽  
Bayes Factor ◽  
Fish Assemblages ◽  
Model Averaging ◽  
External Information ◽  
Bayesian Computation ◽  
Genetic Structuring ◽  
Approximate Bayesian

Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Mol. Ecol. 1998, 7: 499-517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels.

scholarly journals Testing hypotheses of diversification in Panamanian frogs and freshwater fishes using hierarchical approximate Bayesian computation with model averaging

2018 ◽  
Author(s):  
Justin C Bagley ◽  
Michael J Hickerson ◽  
Jerald B Johnson
Keyword(s):  
Freshwater Fish ◽  
Dna Sequences ◽  
Approximate Bayesian Computation ◽  
Bayes Factor ◽  
Fish Assemblages ◽  
Model Averaging ◽  
External Information ◽  
Bayesian Computation ◽  
Genetic Structuring ◽  
Approximate Bayesian

Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Mol. Ecol. 1998, 7: 499-517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels.

scholarly journals Inference of direction, diversity, and frequency of HIV-1 transmission using approximate Bayesian computation

2016 ◽  
Author(s):  
Ethan O. Romero-Severson ◽  
Ingo Bulla ◽  
Nick Hengartner ◽  
Inês Bártolo ◽  
Ana Abecasis ◽  
...  
Keyword(s):  
Approximate Bayesian Computation ◽  
Bayes Factor ◽  
Heterosexual Transmission ◽  
Transmission Model ◽  
Bayesian Computation ◽  
Founding Population ◽  
Abc Method ◽  
Approximate Bayesian ◽  
Prevention Methods ◽  
Hiv 1

ABSTRACTDiversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods and the reconstruction of epidemiologic histories. To measure the diversity of the founding population and to compute the probability of alternative transmission scenarios, while explicitly taking phylogenetic uncertainty into account, we created an Approximate Bayesian Computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity. We applied our method to a heterosexual transmission pair showing a complex paraphyletic-polyphyletic donor-recipient phylogenetic topology. We found evidence identifying the donor that was consistent with the known facts of the case (Bayes factor >20). We also found that while the evidence for ongoing transmission between the pair was as good or better than the singular transmission event model, it was only viable when the rate of ongoing transmission was implausibly high (~1/day). We concluded that the singular transmission model, which was able to estimate the diversity of the founding population (mean 7% substitutions/site), was more biologically plausible. Our study provides a formal inference framework to investigate HIV-1 direction, diversity, and frequency of transmission. The ability to measure the diversity of founding populations in both simple and complex transmission situations is essential to understanding the relationship between the phylogeny and epidemiology of HIV-1 as well as in efforts developing new prevention technologies.

scholarly journals Statistical Inference From Stem Cell Barcoding Data Using Adaptive Approximate Bayesian Computation

2021 ◽  
Author(s):  
Siyi Chen ◽  
Katherine Y. King ◽  
Marek Kimmel
Keyword(s):  
Stem Cell ◽  
Dna Sequences ◽  
Approximate Bayesian Computation ◽  
Sequential Monte Carlo ◽  
Real Life ◽  
Lineage Tracing ◽  
Bayesian Computation ◽  
Multinomial Model ◽  
Hematopoietic Stem ◽  
Approximate Bayesian

Abstract Background: Barcodes that can be supplied to cells by transduction of a library of unique DNA sequences allow identification of heterogeneity in cell populations and lineage tracing applications. Estimation of the number of hematopoietic stem cell (HSC) clones is important since it also allows to approximate the number of hematopoietic stem cells from which the circulating blood cells descend. This problem is similar to the species problem, well-known to ecologists. However, an additional ”degree of freedom” exists, since different HSC generally give rise to clones with different growth rates. This adds credibility to sampling models based on different versions of Dirichlet-multinomial distributions. Results: We developed a truncated population approximate Bayesian computation (ABC) algorithm which is derived from sequential Monte Carlo ABC (SMC-ABC) and applied the method to the symmetric Dirichlet-multinomial model proposed by Zhang et al. (2005) and asymmetric Dirichlet-multinomial model we proposed. Methodology was tested using simulated and real-life data. Conclusions: Results suggest that flexibility of the asymmetric Dirichlet-multinomial helps to obtain insight into heterogeneity of proliferating cell systems such as HSC. Estimates based on experimental data approach the correct count of murine HSC.

River capture or ancestral polymorphism: an empirical genetic test in a freshwater fish using approximate Bayesian computation

2020 ◽  
Vol 131 (3) ◽  
pp. 575-584
Author(s):  
Mateus S Souza ◽  
Andréa T Thomaz ◽  
Nelson J R Fagundes
Keyword(s):  
Mitochondrial Dna ◽  
Freshwater Fish ◽  
Approximate Bayesian Computation ◽  
Large Population ◽  
Secondary Contact ◽  
Bayesian Computation ◽  
Reciprocal Monophyly ◽  
Geological Evidence ◽  
River Capture ◽  
Approximate Bayesian

Abstract A headwater or river capture is a phenomenon commonly invoked to explain the absence of reciprocal monophyly of genetic lineages among isolated hydrographic basins in freshwater fish. Under the assumption of river capture, a secondary contact between populations previously isolated in different basins explains the observed genetic pattern. However, the absence of reciprocal monophyly could also arise under population isolation through the retention of ancestral of polymorphisms. Here, we applied an approximate Bayesian computation (ABC) framework for estimating the relative probability of scenarios with and without secondary contact. We used Cnesterodon decemmaculatus as a study model because of the multiple possible cases of river capture and the demographic parameters estimated in a previous mitochondrial DNA study that are useful for simulating scenarios to test both hypotheses using the ABC framework. Our results showed that, in general, mitochondrial DNA is useful for distinguishing between these alternative demographic scenarios with reasonable confidence, but in extreme cases (e.g. recent divergence or large population size) there is no power to discriminate between scenarios. Testing hypotheses of drainage rearrangement under a statistically rigorous framework is fundamental for understanding the evolution of freshwater fish fauna as a complement to, or in the absence of, geological evidence.

scholarly journals Weighted approximate Bayesian computation via Sanov’s theorem

2021 ◽  
Author(s):  
Cecilia Viscardi ◽  
Michele Boreale ◽  
Fabio Corradi
Keyword(s):  
Large Deviations ◽  
Posterior Distribution ◽  
Approximate Bayesian Computation ◽  
Bayesian Computation ◽  
Information Theoretic ◽  
Discrete Random Variables ◽  
Positive Weights ◽  
Approximate Bayesian ◽  
Information Theoretic Method ◽  
Computational Resources

AbstractWe consider the problem of sample degeneracy in Approximate Bayesian Computation. It arises when proposed values of the parameters, once given as input to the generative model, rarely lead to simulations resembling the observed data and are hence discarded. Such “poor” parameter proposals do not contribute at all to the representation of the parameter’s posterior distribution. This leads to a very large number of required simulations and/or a waste of computational resources, as well as to distortions in the computed posterior distribution. To mitigate this problem, we propose an algorithm, referred to as the Large Deviations Weighted Approximate Bayesian Computation algorithm, where, via Sanov’s Theorem, strictly positive weights are computed for all proposed parameters, thus avoiding the rejection step altogether. In order to derive a computable asymptotic approximation from Sanov’s result, we adopt the information theoretic “method of types” formulation of the method of Large Deviations, thus restricting our attention to models for i.i.d. discrete random variables. Finally, we experimentally evaluate our method through a proof-of-concept implementation.

Flow parameter estimation using laser absorption spectroscopy and approximate Bayesian computation

2021 ◽  
Vol 62 (2) ◽  
Author(s):  
Jason D. Christopher ◽  
Olga A. Doronina ◽  
Dan Petrykowski ◽  
Torrey R. S. Hayden ◽  
Caelan Lapointe ◽  
...  
Keyword(s):  
Parameter Estimation ◽  
Absorption Spectroscopy ◽  
Approximate Bayesian Computation ◽  
Flow Parameter ◽  
Bayesian Computation ◽  
Laser Absorption Spectroscopy ◽  
Laser Absorption ◽  
Approximate Bayesian
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