Abstract
The investigation of genetic clusters in natural populations is an ubiquitous problem in a range of fields relying on the analysis of genetic data, such as molecular ecology, conservation biology and microbiology. Typically, genetic clusters are defined as distinct panmictic populations, or parental groups in the context of hybridisation. Two types of methods have been developed for identifying such clusters: model‐based methods, which are usually computer‐intensive but yield results which can be interpreted in the light of an explicit population genetic model, and geometric approaches, which are less interpretable but remarkably faster.Here, we introduce snapclust, a fast maximum‐likelihood solution to the genetic clustering problem, which allies the advantages of both model‐based and geometric approaches. Our method relies on maximising the likelihood of a fixed number of panmictic populations, using a combination of geometric approach and fast likelihood optimisation, using the Expectation‐Maximisation (EM) algorithm. It can be used for assigning genotypes to populations and optionally identify various types of hybrids between two parental populations. Several goodness‐of‐fit statistics can also be used to guide the choice of the retained number of clusters.Using extensive simulations, we show that snapclust performs comparably to current gold standards for genetic clustering as well as hybrid detection, with some advantages for identifying hybrids after several backcrosses, while being orders of magnitude faster than other model‐based methods. We also illustrate how snapclust can be used for identifying the optimal number of clusters, and subsequently assign individuals to various hybrid classes simulated from an empirical microsatellite dataset. snapclust is implemented in the package adegenet for the free software R, and is therefore easily integrated into existing pipelines for genetic data analysis. It can be applied to any kind of co‐dominant markers, and can easily be extended to more complex models including, for instance, varying ploidy levels. Given its flexibility and computer‐efficiency, it provides a useful complement to the existing toolbox for the study of genetic diversity in natural populations.
Highlights
The identification of groups of genetically related individuals within a population, sensu population subdivision, is an ubiquitous problem in most fields in which genetic data analysis plays an important role including molecular ecology, evolutionary and conservation genetics
We illustrate how snapclust can be used for identifying the optimal number of clusters, and subsequently assign individuals to various hybrid classes simulated from an empirical microsatellite dataset. 4. snapclust is implemented in the package adegenet for the free software R, and is integrated into existing pipelines for genetic data analysis
The likelihood is defined as the probability that the set of genotypes under consideration was generated under a given population structure and model of evolution
Summary
The identification of groups of genetically related individuals within a population, sensu population subdivision, is an ubiquitous problem in most fields in which genetic data analysis plays an important role including molecular ecology, evolutionary and conservation genetics. The main limitation of geometric approaches lies in the fact that their results are harder to interpret biologically These methods typically identify clusters from pairwise genetic distances, without providing group membership probabilities (Jombart et al, 2010; Legendre & Legendre, 2012), so that weak separation between clusters or admixture patterns cannot be distinguished from strong, clear-cut population structure. To some extent, this issue can be addressed, using exploratory approaches such as the DAPC (Jombart et al, 2010), to visualise cluster diversity in a reduced space and even estimate group assignment probabilities, but these probabilities merely reflect genetic proximities, and cannot be interpreted as probabilities that an individual belongs to a given population. Snapclust is implemented in the package adegenet (Jombart, 2008; Jombart & Ahmed, 2011) for the R software (R Core Team 2017), being readily compatible with a wealth of tools for genetic data analysis in R (Goudet, 2005; Jombart et al, 2017; Kamvar, Tabima, & Grünwald, 2014; Paradis, 2010; Popescu, Huber, & Paradis, 2012)
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