scholarly journals Inferring the Effect of Species Interactions on Trait Evolution

2020 ◽  
Author(s):  
Liang Xu ◽  
Sander Van Doorn ◽  
Hanno Hildenbrandt ◽  
Rampal S Etienne

Abstract Models of trait evolution form an important part of macroevolutionary biology. The Brownian motion model and Ornstein–Uhlenbeck models have become classic (null) models of character evolution, in which species evolve independently. Recently, models incorporating species interactions have been developed, particularly involving competition where abiotic factors pull species toward an optimal trait value and competitive interactions drive the trait values apart. However, these models assume a fitness function rather than derive it from population dynamics and they do not consider dynamics of the trait variance. Here, we develop a general coherent trait evolution framework where the fitness function is based on a model of population dynamics, and therefore it can, in principle, accommodate any type of species interaction. We illustrate our framework with a model of abundance-dependent competitive interactions against a macroevolutionary background encoded in a phylogenetic tree. We develop an inference tool based on Approximate Bayesian Computation and test it on simulated data (of traits at the tips). We find that inference performs well when the diversity predicted by the parameters equals the number of species in the phylogeny. We then fit the model to empirical data of baleen whale body lengths, using three different summary statistics, and compare it to a model without population dynamics and a model where competition depends on the total metabolic rate of the competitors. We show that the unweighted model performs best for the least informative summary statistic, while the model with competition weighted by the total metabolic rate fits the data slightly better than the other two models for the two more informative summary statistics. Regardless of the summary statistic used, the three models substantially differ in their predictions of the abundance distribution. Therefore, data on abundance distributions will allow us to better distinguish the models from one another, and infer the nature of species interactions. Thus, our framework provides a conceptual approach to reveal species interactions underlying trait evolution and identifies the data needed to do so in practice. [Approximate Bayesian computation; competition; phylogeny; population dynamics; simulations; species interaction; trait evolution.]

Author(s):  
Hsuan Jung ◽  
Paul Marjoram

In this paper, we develop a Genetic Algorithm that can address the fundamental problem of how one should weight the summary statistics included in an approximate Bayesian computation analysis built around an accept/reject algorithm, and how one might choose the tolerance for that analysis. We then demonstrate that using weighted statistics, and a well-chosen tolerance, in such an approximate Bayesian computation approach can result in improved performance, when compared to unweighted analyses, using one example drawn purely from statistics and two drawn from the estimation of population genetics parameters.


Evolution ◽  
2011 ◽  
Vol 66 (3) ◽  
pp. 752-762 ◽  
Author(s):  
Graham J. Slater ◽  
Luke J. Harmon ◽  
Daniel Wegmann ◽  
Paul Joyce ◽  
Liam J. Revell ◽  
...  

Author(s):  
Yang Zeng

Abstract Due to the flexibility and feasibility of addressing ill-posed problems, the Bayesian method has been widely used in inverse heat conduction problems (IHCPs). However, in the real science and engineering IHCPs, the likelihood function of the Bayesian method is commonly computationally expensive or analytically unavailable. In this study, in order to circumvent this intractable likelihood function, the approximate Bayesian computation (ABC) is expanded to the IHCPs. In ABC, the high dimensional observations in the intractable likelihood function are equalized by their low dimensional summary statistics. Thus, the performance of the ABC depends on the selection of summary statistics. In this study, a machine learning-based ABC (ML-ABC) is proposed to address the complicated selections of the summary statistics. The Auto-Encoder (AE) is a powerful Machine Learning (ML) framework which can compress the observations into very low dimensional summary statistics with little information loss. In addition, in order to accelerate the calculation of the proposed framework, another neural network (NN) is utilized to construct the mapping between the unknowns and the summary statistics. With this mapping, given arbitrary unknowns, the summary statistics can be obtained efficiently without solving the time-consuming forward problem with numerical method. Furthermore, an adaptive nested sampling method (ANSM) is developed to further improve the efficiency of sampling. The performance of the proposed method is demonstrated with two IHCP cases.


2016 ◽  
Vol 43 (12) ◽  
pp. 2191-2202 ◽  
Author(s):  
Muhammad Faisal ◽  
Andreas Futschik ◽  
Ijaz Hussain ◽  
Mitwali Abd-el.Moemen

Author(s):  
Théophile Sanchez ◽  
Jean Cury ◽  
Guillaume Charpiat ◽  
Flora Jay

AbstractFor the past decades, simulation-based likelihood-free inference methods have enabled researchers to address numerous population genetics problems. As the richness and amount of simulated and real genetic data keep increasing, the field has a strong opportunity to tackle tasks that current methods hardly solve. However, high data dimensionality forces most methods to summarize large genomic datasets into a relatively small number of handcrafted features (summary statistics). Here we propose an alternative to summary statistics, based on the automatic extraction of relevant information using deep learning techniques. Specifically, we design artificial neural networks (ANNs) that take as input single nucleotide polymorphic sites (SNPs) found in individuals sampled from a single population and infer the past effective population size history. First, we provide guidelines to construct artificial neural networks that comply with the intrinsic properties of SNP data such as invariance to permutation of haplotypes, long scale interactions between SNPs and variable genomic length. Thanks to a Bayesian hyperparameter optimization procedure, we evaluate the performance of multiple networks and compare them to well established methods like Approximate Bayesian Computation (ABC). Even without the expert knowledge of summary statistics, our approach compares fairly well to an ABC based on handcrafted features. Furthermore we show that combining deep learning and ABC can improve performance while taking advantage of both frameworks. Finally, we apply our approach to reconstruct the effective population size history of cattle breed populations.


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