Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis

By Arnaud Estoup, Philippe Jarne, Jean-Marie Cornuet. Molecular Ecology, 2002

930 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f7f9a0b267a279ce7d8acb001336dfff1f4b738e

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In Genetics

Citations in the corpus

Maize association population: a high-resolution platform for quantitative trait locus dissection. (2005, background): “…that exists at microsatellite loci may bias Fst estimates and detection of population structure, this is not usually considered to represent a significant problem, as the large amount of variability at microsatellite loci often compensates for the existence of homoplasy (Estoup et al., 2002).”
Population structure and long-range linkage disequilibrium in a durum wheat elite collection (2005, neutral): “Highly polymorphic dinucleotides were preferred over triand tetra-nucleotides in order to limit the risk of allelic homoplasy (presence of alleles similar in state, but not identical by descent; Estoup et al. 2002), a condition less likely to occur with dinucleotide SSRs (Matsuoka et al.”
Microsatellites: simple sequences with complex evolution (2004, neutral): “Note that in contrast to base substitutions, for which an infinite allele model is applicable, microsatellite alleles are often identical in state (structure) but not by descen”
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0) (2010, background): “Due to their mutation modalities (high mutation rates with allele size homoplasy and constraints [37]), it is not surprising that microsatellite loci performed poorly for ancient evolutionary events [51,52].”
Genetic structure of montane isolates of Pinus sylvestris L. in a Mediterranean refugial area (2005, background): “Its effects on the inferred genetic and phylogeographical structure, mimicking shared ancestry or gene exchange, remain difficult to circumvent (Goldstein & Pollock, 1997), although phylogenetic reconstructions among closely related populations would be somewhat less affected by the mutation model a”
POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. (2010, background): “Recently, because of the high degree of genetic polymorphism, microsatellite DNA data (Estoup et al. 2002; DeSalle and Amato 2004) are widely used for genetic studies of populations in various organisms.”
Methods for Development of Microsatellite Markers: An Overview (2014, neutral): “Homoplasy is another problem when applying microsatellites as a reliable tool for phylogenetic analysis because alleles considered to be identical in state are not necessarily identical by descent (Estoup et al., 2002).”
Status and Prospects of Association Mapping in Plants (2008, background): “If alleles have a high mutation rate and strong size constraint, SSR size homoplasy could be problematic when estimating genetic parameters in a large population (Estoup et al., 2002).”
Genetic homogeneity in Juglans nigra (Juglandaceae) at nuclear microsatellites (2006, background): “Size homoplasy at microsatellite loci can lead to significant underestimation of genetic differentiation (Estoup et al., 2002).”
Origin, evolution and genome distribution of microsatellites (2006, background): “Homoplasy may seriously influence population studies involving high mutation rates and large population sizes together with strong allele size constraints (Estoup et al., 2002).”
OPERATIONAL CRITERIA FOR DELIMITING SPECIES (2004, background): “Both allozyme (Murphy et al. 1996) and microsatellite loci (Li et al. 2002, Estoup et al. 2002) can be characterized by allelic homoplasy between closely related species, which will introduce an unknown error into the use of either kind of data in FFR methods.”
Symbiodinium sp. associations in the gorgonian Pseudopterogorgia elisabethae in the Bahamas: high levels of genetic variability and population structure in symbiotic dinoflagellates (2003, background): “Although microsatellite alleles may sometimes violate this assumption (e.g. Viard et al. 1998), the occurrence of size homoplasy (alleles identical in state, but not identical by descent) is not considered a significant problem for analyses of population genetic structure (Estoup et al. 2002).”