spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels

By Olivier J. Hardy, X. Vekemans. 2002

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In Genetics

Citations in the corpus

Extent and Reproductive Mechanisms of Phragmites australis Spread in Brackish Wetlands in Chesapeake Bay, Maryland (USA) (2010, background): “2 g, Hardy and Vekemans 1999, 2002) to calculate genetic similarity between patches.”
Spread of invasive Phragmites australis in estuaries with differing degrees of development: genetic patterns, Allee effects and interpretation (2010, background): “2 g; Hardy & Vekemans 1999, 2002) at distances of 10, 50, 100, 500, 1000 and 50 000 m. Distance classes were chosen to incorporate a range of within and among-patch Euclidean distances while maintaining adequate numbers of sample pairs (>100) within each distance class.”
Genetic isolation by distance and landscape connectivity in the American marten (Martes americana) (2006, positive): “Genetic distances between individuals (a) were computed with the program SPAGeDI (Hardy and Vekemans 2002).”
Genetic similarity of social mates predicts the level of extrapair paternity in splendid fairy-wrens (2005, methodology): “We estimated genetic similarity as pairwise relatedness between breeding females and their mates with the program SPAGeDi 1.0 (Hardy & Vekemans 2002) using a ‘twogenes’ relationship coefficient, r, based on Queller & Goodnight’s (1989) formula.”
Dispersal Patterns of Orang-utans (Pongo spp.) in a Bornean Peat-swamp Forest (2011, neutral): “We calculated 4 different relatedness indices (Li et al. 1993; Lynch and Ritland 1999; Queller and Goodnight 1989; Wang 2002) for all pairs of individuals using SPAGeDi (Hardy and Vekemans 2002).”
coancestry: a program for simulating, estimating and analysing relatedness and inbreeding coefficients (2011, methodology): “…inbreeding in captive populations (e.g. Jones et al. 2002; Sekino et al. 2004), studying spatial structure and isolation by distance (e.g. Hardy & Vekemans 2002; Vekemans & Hardy 2004), examining social structures and kin selection (e.g. Girman et al. 1997; Peters et al. 1999), inferring…”
New insights from fine‐scale spatial genetic structure analyses in plant populations (2004, methodology): “The process is repeated until successive ; estimates stabilize (procedure implemented in the software spagedi; Hardy and Vekemans 2002; http://http://www.ulb.ac.be/sciences/lagev).”
Landscape genetics: combining landscape ecology and population genetics (2003, neutral): “(http://www.ulb.ac.be/sciences/lagev/software.html) [ 60 ]”
Sweet Sorghum Genetic Diversity and Association Mapping for Brix and Height (2009, methodology): “Using the package SPAGeDi 1.2 (Hardy and Vekemans, 2002), a kinship coeffi cient estimation matrix was created according to J. Nason (described in Loiselle et al., 1995).”
A Mutation in the Myostatin Gene Increases Muscle Mass and Enhances Racing Performance in Heterozygote Dogs (2007, neutral): “2f [28].”
An Arabidopsis Example of Association Mapping in Structured Samples (2006, methodology): “The former contains the relative kinship coefficients of Ritland [24] estimated using SPAGeDi [49] from about 12,000 nonsingleton SNPs identified by Nordborg et al.”
High gene flow in oceanic bottlenose dolphins (Tursiops truncatus) of the North Atlantic (2007, positive): “Mean degree of relatedness between resident individuals was compared to mean relatedness in the Azores based on Moran’s I coefficients calculated with SPAGeDi 1.1b ( Hardy and Vekemans 2002 ).”
A unified mixed-model method for association mapping that accounts for multiple levels of relatedness (2006, methodology): “The relative kinship (K) matrix was calculated on the basis of 553 SNPs using the software package SPAGeD”
Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance? (2009, methodology): “The linear regression slope, b , of this relationship offers a convenient measure of the degree of spatial genetic structuring (Hardy & Vekemans 2002).”
Rainbow trout (Oncorhynchus mykiss) invasion and the spread of hybridization with native westslope cutthroat trout (Oncorhynchus clarkii lewisi) (2008, methodology): “We used the allele size permutation procedure in program SPAGeDi (Hardy and Vekemans 2002; Hardy et al. 2003) to test whether mutations contributed significantly to population divergence.”
Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize (2011, methodology): “Finally, the relative kinship coefficients were calculated using the SPAGeDi software package (Hardy and Vekemans 2002).”