Bayesian spatial modeling of genetic population structure

Corander, Jukka; Sirén, Jukka; Arjas, Elja

doi:10.1007/s00180-007-0072-x

Cited by 389 publications

(357 citation statements)

References 23 publications

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“…In the original methods developed by Pritchard et al (2000), Dawson and Belkhir (2001) and Corander et al (2003), spatial information was not explicitly included in the modeling. However, some recent Bayesian assignment methods incorporate information from the geographical coordinates of individuals, by using prior distributions for the spatial distribution of individuals in a cluster (Wasser et al, 2004;Guillot et al, 2005;François et al, 2006;Corander et al, 2008). Simulation studies have shown that incorporation of geographical information into assignment methods can result in better statistical performance (Chen et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

et al. 2009

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We have investigated the fine-scale spatial genetic structure in a managed Scots pine forest. For this purpose, we perform a Bayesian genetic-cluster analysis of 96 geographically mapped individual seed trees of Swedish Scots pine based on 14 microsatellite loci. The analysis was carried out with the recently developed program GENECLUST (François et al., 2006), which provides the facility to jointly incorporate both spatial information from a geographical neighborhood structure through a Potts-Dirichlet model and account for variable degrees of inbreeding within the clusters. To evaluate whether inbreeding and spatial interaction should be included in the best-fitting statistical model for our data, we used the deviance information criterion (DIC), a weighted measure of model fit that accounts for an effective number of free parameters in a model. Analysis shows that a model with a single estimated cluster, with high levels of inbreeding (0.25) and with a moderate amount of spatial dependency within the unique cluster (C ¼ 0.2-0.4), best explains the data. We also carried out Bayesian parentage analysis, which enabled us to exclude the possibility that the sample constitutes one single full-sib family.

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Section: Introductionmentioning

confidence: 99%

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

et al. 2009

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“…To examine if the resulting genetic structure was correlated with geographical distribution, Mantel's tests were performed with GenAlEx 6.5 (10 permutations). Moreover, a spatial Bayesian clustering algorithm was applied using BAPS 5.2 (Corander et al 2008;Cheng et al 2013) and performing 10 independent runs for each lvalue (1-20). The resulting partitions were visualized as Voronoi diagrams (tessellations).…”

Section: Genetic Structurementioning

confidence: 99%

Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in northwestern Spain

Quintana

Contreras

Merino

et al. 2014

Tree Genetics & Genomes

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This paper presents a detailed genetic study of Castanea sativa in El Bierzo, a major nut production region with interesting features. It is located within a glacial refuge at one extreme of the distribution area (northwest Spain); it has a centenary tradition of chestnut management; and more importantly, it shows an unusual degree of genetic isolation. Seven nuclear microsatellite markers were selected to analyze the genetic variability and structure of 169 local trees grafted for nut production. We analyzed in the same manner 62 local nuts. The selected loci were highly discriminant for the genotypes studied, giving a combined probability of identity of 6.1 x 10~6. An unprecedented density of trees was sampled for this project over the entire region, and nuts were collected representing 18 cultivars marketed by local producers. Several instances of misclassification by local growers were detected. Fixation index estimates and analysis of molecular variance (AMOVA) data are supportive of an unexpectedly high level of genetic differentiation in El Bierzo, larger than that estimated in a previous study with broader geographical scope but based on limited local sampling (Pereira-Lorenzo et al., Tree Genet Genomes 6: 701-715, 2010a). Likewise, we have determined that clonality due to grafting had been previously overestimated. In line with these observations, no significant spatial structure was found using both a modelbased Bayesian procedure and Mantel's tests. Taken together, our results evidence the need for more fine-scale genetic studies if conservation strategies are to be efficiently improved.

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“…Bayesian identification of genotype pools in U. laevis Two Bayesian clustering programs were used to assess population structure in the microsatellite data set: STRUCTURE v.2.1 (Pritchard et al, 2000) and BAPS v.4.0 (Corander et al, 2008). First, we used STRUCTURE to reveal individualbased patterns in genetic variation without prior information on sample geographic origin.…”

Section: Dna Extraction and Scoring Of Molecular Markersmentioning

confidence: 99%

Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

Fuentes-Utrilla¹,

Venturas²,

Hollingsworth³

et al. 2013

Heredity

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Conservation policies usually focus on in situ protection of native populations, a priority that requires accurate assessment of population status. Distinction between native and introduced status can be particularly difficult (and at the same time, is most important) for species whose natural habitat has become both rare and highly fragmented. Here, we address the status of the white elm (Ulmus laevis Pallas), a European riparian tree species whose populations have been fragmented by human activity and is protected wherever it is considered native. Small populations of this species are located in Iberia, where they are unprotected because they are considered introductions due to their rarity. However, Iberia and neighbouring regions in southwestern France have been shown to support discrete glacial refuge populations of many European trees, and the possibility remains that Iberian white elms are native relicts. We used chloroplast RFLPs and nuclear microsatellites to establish the relationship between populations in Iberia and the Central European core distribution. Bayesian approaches revealed significant spatial structure across populations. Those in Iberia and southwestern France shared alleles absent from Central Europe, and showed spatial population structure within Iberia common in recognized native taxa. Iberian populations show a demographic signature of ancient population bottlenecks, while those in Central European show a signature of recent population bottlenecks. These patterns are not consistent with historical introduction of white elm to Iberia, and instead strongly support native status, arguing for immediate implementation of conservation measures for white elm populations in Spain and contiguous areas of southern France.

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Bayesian spatial modeling of genetic population structure

Abstract: Bayesian inference, Genetic structure, Spatial modeling, Statistical learning theory, Unsupervised classification,

Cited by 389 publications

References 23 publications

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in northwestern Spain

Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

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