Using AFLP markers and the Geneland program for the inference of population genetic structure

@article{Guillot2010UsingAM,
  title={Using AFLP markers and the Geneland program for the inference of population genetic structure},
  author={Gilles Guillot and Filipe Santos},
  journal={Molecular Ecology Resources},
  year={2010},
  volume={10}
}
The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how the computer program Geneland designed to infer population structure has been adapted to deal with dominant markers; and (ii) we use Geneland for numerical comparison of dominant and codominant markers to… 
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References

SHOWING 1-10 OF 23 REFERENCES
Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis
TLDR
Comparing the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of codominant multiallelic markers,such as microsatellites, in reconstructing parentage shows dominant markers are less efficient thancodominant markers for achieving this, but can be used with good confidence.
An Approximate Bayesian Computation Approach to Overcome Biases That Arise When Using Amplified Fragment Length Polymorphism Markers to Study Population Structure
TLDR
A new Bayesian method is presented that estimates population-specific FIS and FST values and offers users the possibility of taking into account the criteria for selecting the markers that are used in the analyses, and provides advice on how to avoid the effects of ascertainment bias.
Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists
TLDR
This review describes the various methods available to handle AFLP data, and investigates the characteristics and limitations of these statistical tools, and appeals for a wider adoption of methodologies borrowed from other research fields, like for example those especially designed to deal with binary data.
AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites
TLDR
The case study showed that given a comparable analytical effort in the laboratory, AFLP were much more efficient than the microsatellites in discriminating the source of an individual among putative populations, especially in systems characterized by weak population structuring.
On the Informativeness of Dominant and Co-Dominant Genetic Markers for Bayesian Supervised Clustering
TLDR
This work suggests that dominant markers studies can achieve an accuracy similar to that of codominant markers studies if the number of markers used in the former is about 1.7 times larger than in the latter.
Correcting for ascertainment bias in the inference of population structure
TLDR
This work shows how an Markov chain Monte Carlo algorithm known as single variable exchange algorithm (SVEA) can be implemented for a class of clustering models of broad interest in population genetics that includes the models underlying the computer programs STRUCTURE, GENELAND and GESTE.
Inference of structure in subdivided populations at low levels of genetic differentiation - the correlated allele frequencies model revisited
TLDR
A Markov chain Monte Carlo algorithm and a new post-processing scheme are proposed that significantly improve the accuracy of previously existing algorithms in terms of estimated number of populations and estimated population membership.
Genes mirror geography within Europe
TLDR
Despite low average levels of genetic differentiation among Europeans, there is a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans.
A Spatial Statistical Model for Landscape Genetics
TLDR
A Bayesian model implemented in a Markov chain Monte Carlo scheme that allows inference of the location of such genetic discontinuities from individual geo-referenced multilocus genotypes, without a priori knowledge on populational units and limits is described.
Assigning African elephant DNA to geographic region of origin: applications to the ivory trade.
TLDR
A combined genetic and statistical method to determine the origin of poached ivory by exploiting a smoothing method to estimate geographic-specific allele frequencies over the entire African elephants' range, which are used to infer the geographic origin of DNA samples, such as could be obtained from tusks of unknown origin.
...
1
2
3
...