Journal ArticleDOI
genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms
TLDR
Two programs, GENOTYPE and GENODIVE, developed for analyses of clonal diversity in asexually reproducing organisms, show that genotype can be used for detecting genotyping errors in studies of sexual organisms.Abstract:
Investigating diversity in asexual organisms using molecular markers involves the assignment of individuals to clonal lineages and the subsequent analysis of clonal diversity. Assignment is possible using a distance matrix in combination with a user-specified threshold, defined as the maximum distance between two individuals that are considered to belong to the same clonal lineage. Analysis of clonal diversity requires tests for differences in diversity and clonal composition between populations. We developed two programs, GENOTYPE and GENODIVE for such analyses of clonal diversity in asexually reproducing organisms. Additionally, genotype can be used for detecting genotyping errors in studies of sexual organisms.read more
Citations
More filters
Journal ArticleDOI
GenAlEx 6.5
Rod Peakall,Peter E. Smouse +1 more
TL;DR: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel that offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.
Journal ArticleDOI
Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.
TL;DR: The R package poppr is developed providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations, and functions for genotypic diversity and clone censoring are specific for clonal populations.
Journal ArticleDOI
DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors
TL;DR: A new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (θ, GST) and population differentiation statistics (DJost, GST ' , χ2 test for population heterogeneity), among others.
Journal ArticleDOI
Assessing population structure: FST and related measures
TL;DR: In this paper, the relationship between the three classes of statistics (F(ST), F'(ST) and D), their estimation and their properties is discussed, and the authors illustrate the relationships between the statistics using a data set of estimates from 84 species taken from the last 4 years of Molecular Ecology.
Journal ArticleDOI
Increased genetic variation and evolutionary potential drive the success of an invasive grass.
Sébastien Lavergne,Jane Molofsky +1 more
TL;DR: The results show that repeated introductions of a single species may inadvertently create harmful invaders with high adaptive potential, and multiple immigration events may trigger future adaptation and geographic spread of a species population by preventing genetic bottlenecks and generating genetic novelties through recombination.
References
More filters
Book
Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Book
Randomization and Monte Carlo methods in biology
TL;DR: This book discusses the construction of tests in non-standard situations testing for randomness of species co-occurences on islands examining time change in niche ovelap probing multivariate data with random skewers other examples.
Journal ArticleDOI
gimlet: a computer program for analysing genetic individual identification data
TL;DR: Gimlet is a user-friendly software package designed to perform several simple tasks, including construction of consensus genotypes from repeated genotyping, estimation of genotypes error rates, and estimation of several population parameters such as allele frequencies, heterozygosity, probability of identity, and population size.
Journal ArticleDOI
mlgsim: a program for detecting clones using a simulation approach
TL;DR: The evolution of Otiorynchid weevils, mainly Otiorhynchus scaber and sulcatus is examined in an attempt to trace the evolutionary history and find out what causes the variation in success of different parthenogens.
Related Papers (5)
Inference of population structure using multilocus genotype data
Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.
genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
Rodney Peakall,Peter E. Smouse +1 more