GeneticStudio: a suite of programs for spatial analysis of genetic-marker data (original) (raw)
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GenVectors: an integrative analytical tool for spatial genetics
Metapopulations are sets of local populations connected by dispersal. While genetic turnover informs about the number of alleles shared by (meta)populations, a set of populations that do not share alleles with a second set may still show low genetic divergence to it. Recent secondary contact driven by anthropogenic habitat fragmentation and/or current climate change, for instance, may erase the historical track of genetic turnover. On the other hand, genetic turnover among sets of populations is expected to be related to the degree of genetic divergence among them if metapopulations become isolated from others due to vicariance or ancient dispersal. Yet, current analytical tools do not permit direct inference about alternative processes underlying spatial, environmental and/or biogeographic correlates of genetic turnover among populations. We introduce GenVectors, a new R package that offers flexible analytical tools that allow evaluating biogeographic or environmental correlates of...
adegenet: a R package for the multivariate analysis of genetic markers
The package adegenet for the R software is dedicated to the multivariate analysis of genetic markers. It extends the ade4 package of multivariate methods by implementing formal classes and functions to manipulate and analyse genetic markers. Data can be imported from common population genetics software and exported to other software and R packages. adegenet also implements standard population genetics tools along with more original approaches for spatial genetics and hybridization. Availability: Stable version is available from CRAN: http://cran. r-project.org/mirrors.html. Development version is available from adegenet website: http://adegenet.r-forge.r-project.org/. Both versions can be installed directly from R. adegenet is distributed under the GNU General Public Licence
genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
Molecular Ecology Notes, 2006
genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include amova, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and twogener. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, genalex 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/
Using AFLP markers and the Geneland program for the inference of population genetic structure
Molecular Ecology Resources, 2010
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 perform clustering. AFLP markers lead to less accurate results than bi‐allelic codominant markers such as single nucleotide polymorphisms (SNP) markers but this difference becomes negligible for data sets of common size (number of individuals n≥100, number of markers L≥200). The latest Geneland version (3.2.1) handling dominant markers is freely available as an R package with a fully clickable graphical interface. Installation instructions and documentation can be found on http://www2.imm.dtu.dk/\~g...
GenoCline: On the trail of spatial patterns of genetic variation
2020
The accurate determination of the spatial trends on the variability of the gene pool of a species is essential to elucidate the underlying demographic-evolutionary events and, ultimately, to unravel the microevolutionary history of the species or population under examination. In this work, we present a new software tool called GenoCline, which is essentially devised to assist in detecting genetic clines from allele and phenotypic frequency data, and even from genome-wide data. This program package allows identifying the geographic orientation of clinal genetic variation through a system of iterative rotation of a virtual coordinate axis. At the same time, GenoCline can also be used to carry out complementary statistical analyses aimed at clarifying the potential origin of the genetic clines found, among which stand out spatial autocorrelation, isolation by distance, centroid method, multidimensional scaling and Sammon projection. Among the main advantages of this software are those related to ease in data entry and potential interconnection with other programs. Data entry is user-friendly. Genetic frequencies and geographic coordinates can be easily entered in spreadsheet table formatting, while genome-wide data can be imported in Eigensoft format. Genetic frequencies can also be exported in a format compatible with other programs dealing with population genetics and evolutionary biology. All illustrations of results are saved in eps format so that there will be high quality and easily editable vectorial graphs available for the researcher. GenoCline is implemented in Java, so it can be used with different operating systems.
With the advent of RFLPs, genetic linkage maps are now being assembled for a number of organisms including both inbred experimental populations such as maize and outbred natural populations such as humans. Accurate construction of such genetic maps requires multipoint linkage analysis of particular types of pedigrees. We describe here a computer package, called MAPMAKER, designed specifically for this purpose. The program uses an efficient algorithm that allows simultaneous multipoint analysis of any number of loci. MAPMAKER also includes an interactive command language that makes it easy for a geneticist to explore linkage data. MAPMAKER has been applied to the construction of linkage maps in a number of organisms, including the human and several plants, and we outline the mapping strategies that have been used.
Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity
Molecular Ecology Resources, 2011
The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS Ò , to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input fi les, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
GGT 2.0: Versatile Software for Visualization and Analysis of Genetic Data
Journal of Heredity, 2008
Ever since its first release in 1999, the free software package for visualization of molecular marker data, graphical genotype (GGT), has been constantly adapted and improved. The GGT package was developed in a plantbreeding context and thus focuses on plant genetic data but was not intended to be limited to plants only. The current version has many options for genetic analysis of populations including diversity analyses and simple association studies. A second release of the GGT package, GGT 2.0 (available through http://www.plantbreeding.wur.nl), is therefore presented in this paper. An overview of existing and new features that are available within GGT 2.0, and a case study in which GGT 2.0 is applied to analyze an existing set of plant genetic data, are presented and discussed.
Journal of Heredity, 2005
Recently different studies have formalized the way in which it is possible to obtain coancestry coefficients from molecular information (Caballero and Toro 2002; Eding and Meuwissen 2001) by applying Malécot's (1948) definition of kinship to marker genes, though referring it to identity-by-state instead of identity-by-descent (Caballero and Toro 2002). The molecular coancestry between two individuals, i and j, is the probability that two randomly sampled alleles from the same locus in two individuals are identical by state. Because of its straightforward relationship with genealogical coancestry, this parameter has been shown to have interesting properties that may be used for conservation purposes (Eding et al. 2002; Toro et al., 2002; 2003). Moreover, molecular coancestry can be used to assess genetic diversity within and between populations (Eding and Meuwissen 2001). Using simulated data, Eding and Meuwissen (2001) showed that molecular coancestry has some interesting properties, namely that average kinship between populations becomes constant very quickly after population fission, causing between-population diversity to remain constant. This property allows researchers using molecular coancestry information to study the genetic relationships between populations (Á lvarez et al. 2005; Caballero and Toro 2002; Fabuel et al. 2004). Despite the utility of molecular coancestry for conservation worth and evolutionary studies, no computer routines are available to facilitate the use of molecular coancestry information. MolKin (version 2.0) is a population genetics computer program that conducts several genetic analyses on multilocus information in a user-friendly environment. The program will help researchers or those responsible for population management to assess genetic variability and population structure at reduced costs with respect to dataset