2BAD: an application to estimate the parental contributions during two independent admixture events

  title={2BAD: an application to estimate the parental contributions during two independent admixture events},
  author={Timothy C. Bray and V. C. Sousa and B{\'a}rbara Parreira and Michael William Bruford and Loun{\`e}s Chikhi},
  journal={Molecular Ecology Resources},
Several approaches have been developed to calculate the relative contributions of parental populations in single admixture event scenarios, including Bayesian methods. In many breeds and populations, it may be more realistic to consider multiple admixture events. However, no approach has been developed to date to estimate admixture in such cases. This report describes a program application, 2BAD (for 2‐event Bayesian ADmixture), which allows the consideration of up to two independent admixture… 

Population divergence with or without admixture: selecting models using an ABC approach

This work applied an approximate Bayesian computation (ABC) approach to select the model that best fits microsatellite data among alternative splitting and admixture models and suggests that the observed genetic patterns are better explained by a population split model without admixture.

Admixture analysis in relation to pedigree studies of introgression in a minority British cattle breed: the Lincoln Red.

It is suggested ABC methods are a valuable supplement to pedigree-based studies but that the accuracy of admixture determination is likely to diminish with increasing complexity of the admixture scenario.

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

The results show that all three factors (genetic differentiation/gene flow, genetic diversity, and the sampling scheme) play a role in generating false bottleneck signals, and suggest an ad hoc method to counter this effect.

Approximate Bayesian Computation in Evolution and Ecology

Although the method arose in population genetics, ABC is increasingly used in other fields, including epidemiology, systems biology, ecology, and agent-based modeling, and many of these applications are briefly described.

Tests of two methods for identifying founder effects in metapopulations reveal substantial type II error

Simulations of hypothetical metapopulations show that population recovery can rapidly eliminate the statistical signature of a bottleneck, and that moderate levels of gene flow can generate a false signal of recent population growth for demes in equilibrium.

Computation in Evolution and Ecology

Although the method arose in population genetics, ABC is increasingly used in other fields, including epidemiology, systems bi- ology, ecology, and agent-based modeling, and many of these applications are briefly described.

Approximate Bayesian Computation

Approximate Bayesian computation (ABC) constitutes a class of computational methods rooted in Bayesian statistics that widen the realm of models for which statistical inference can be considered and exacerbates the challenges of parameter estimation and model selection.

An Approximate Likelihood Perspective on ABC Methods

This article provides a unifying review, general representation, and classification of all ABC methods from the view of approximate likelihood theory, which clarifies how ABC methods can be characterized, related, combined, improved, and applied for future research.

abc: an R package for approximate Bayesian computation (ABC)

Approximate Bayesian computation (ABC) is devoted to complex models because it bypasses the evaluation of the likelihood function by comparing observed and simulated data.



Maximum-likelihood estimation of admixture proportions from genetic data.

A likelihood method is proposed to estimate jointly the admixture proportions, the genetic drift that occurred to the admixed population and each parental population during the period between the hybridization and sampling events, and the genetic Drift in each ancestral population within the interval between their split and hybridization.

Bayesian Analysis of an Admixture Model With Mutations and Arbitrarily Linked Markers

The application of the approximate Bayesian computation (ABC) framework to an artificially admixed domestic bee population from northwest Italy suggests that the admixture occurred in the last 10–40 generations and that the parental Apis mellifera and A. ligustica populations were completely separated since the last glacial maximum.

Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo.

A new method is developed, which allows the simultaneous estimation of the time since the admixture event and the contribution of one of two parental populations (which the method calls p1) and the joint estimation of drift and p1 can provide additional insights into the data.

Approximate Bayesian Computation Without Summary Statistics: The Case of Admixture

Results show that in general ABC provides good approximations to the posterior distributions obtained with the full-likelihood method, suggesting that it is possible to apply ABC using allele frequencies to make inferences in cases where it is difficult to select a set of suitable summary statistics and when the complexity of the model or the size of the data set makes it computationally prohibitive to use full- likelihood methods.

Estimating admixture proportions with microsatellites: comparison of methods based on simulated data

A simulated data‐based comparison of six of the most cited methods in the literature of the last 20 years to estimate the parental contributions in the genetic pool of an admixed population of honeybee populations finds no method is always better or worse than all others.

The population genetic effects of ancestry and admixture in a subdivided cattle breed.

The inconsistency of estimation of admixture proportions between the methods highlights the potentially confounding role of genetic drift in shaping small population structure, and the consequences of accurately describing population histories from contemporary genetic data.

Approximate Bayesian computation in population genetics.

A key advantage of the method is that the nuisance parameters are automatically integrated out in the simulation step, so that the large numbers of nuisance parameters that arise in population genetics problems can be handled without difficulty.

Statistical evaluation of alternative models of human evolution

Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, it is shown that a simple African replacement model with exponential growth has a higher probability as compared with alternative multiregional evolution or assimilation scenarios.

Geographic Patterns of Genome Admixture in Latin American Mestizos

An analysis of admixture in thirteen Mestizo populations from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites found extensive variation in Native American and European ancestry among populations and individuals and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women.

Generating samples under a Wright-Fisher neutral model of genetic variation

A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model, and the samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.