BAPS 2: enhanced possibilities for the analysis of genetic population structure

Corander, Jukka; Waldmann, Patrik; Marttinen, Pekka; Sillanpää, Mikko J.

doi:10.1093/bioinformatics/bth250

Cited by 429 publications

(432 citation statements)

References 24 publications

(57 reference statements)

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“…Since group-level analysis does not rely on the integrity of individual multilocus genotypes, we were able to use the method to compare solutions from the original and null-allele-corrected data sets. The resulting clusters (from the original data set) were saved, and admixture proportions-estimated for each individual, again using BAPS 4.13 (Corander et al 2004), with the posterior probability for the null hypothesis of pure ancestry-were computed by permutation. We used clusters, rather than individual sample sites, as the units for the analysis because admixture results can be unreliable when the power to discriminate populations is low ( J.…”

Section: Methodsmentioning

confidence: 99%

Ecological Zones Rather Than Molecular Forms Predict Genetic Differentiation in the Malaria VectorAnopheles gambiaes.s. in Ghana

et al. 2007

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The malaria mosquito Anopheles gambiae s.s. is rapidly becoming a model for studies on the evolution of reproductive isolation. Debate has centered on the taxonomic status of two forms (denoted M and S) within the nominal taxon identified by point mutations in the X-linked rDNA region. Evidence is accumulating that there are significant barriers to gene flow between these forms, but that the barriers are not complete throughout the entire range of their distribution. We sampled populations from across Ghana and southern Burkina Faso, West Africa, from areas where the molecular forms occurred in both sympatry and allopatry. Neither Bayesian clustering methods nor F ST -based analysis of microsatellite data found differentiation between the M and S molecular forms, but revealed strong differentiation among different ecological zones, irrespective of M/S status and with no detectable effect of geographical distance. Although no M/S hybrids were found in the samples, admixture analysis detected evidence of contemporary interform gene flow, arguably most pronounced in southern Ghana where forms occur sympatrically. Thus, in the sampled area of West Africa, lack of differentiation between M and S forms likely reflects substantial introgression, and ecological barriers appear to be of greater importance in restricting gene flow.

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Section: Methodsmentioning

confidence: 99%

Ecological Zones Rather Than Molecular Forms Predict Genetic Differentiation in the Malaria VectorAnopheles gambiaes.s. in Ghana

et al. 2007

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“…We also examined the genetic clustering of samples using BAPS V4.14 (Corander et al 2004), STRUCTURE V2.3.2 (Pritchard et al 2000), and by performing an analysis of molecular variation (AMOVA). BAPS (Corander et al 2004) uses Bayesian mixture modeling to describe variation within subpopulations using a separate joint probability distribution over multiple loci. The mixture model parameters include the assignment of individuals to clusters to optimize genetic similarity within clusters.…”

Section: Genetic Variation and Population Structurementioning

confidence: 99%

Effective population size is strongly correlated with breeding pond size in the endangered California tiger salamander, Ambystoma californiense

Wang

Johnson

et al. 2011

Conserv Genet

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Maintaining genetic diversity and population viability in endangered and threatened species is a primary concern of conservation biology. Genetic diversity depends on population connectivity and effective population size (N e ), both of which are often compromised in endangered taxa. While the importance of population connectivity and gene flow has been well studied, investigating effective population sizes in natural systems has received far less attention. However, N e plays a prominent role in the maintenance of genetic diversity, the prevention of inbreeding depression, and in determining the probability of population persistence. In this study, we examined the relationship between breeding pond characteristics and N e in the endangered California tiger salamander, Ambystoma californiense. We sampled 203 individuals from 10 breeding ponds on a local landscape, and used 11 polymorphic microsatellite loci to quantify genetic structure, gene flow, and effective population sizes. We also measured the areas of each pond using satellite imagery and classified ponds as either hydrologically-modified perennial ponds or naturally occurring vernal pools, the latter of which constitute the natural breeding habitat for A. californiense. We found no correlation between pond area and heterozygosity or allelic diversity, but we identified a strong positive relationship between breeding pond area and N e , particularly for vernal pools. Our results provide some of the first empirical evidence that variation in breeding habitat can be associated with differences in N e and suggest that a more complete understanding of the environmental features that influence N e is an important component of conservation genetics and management.

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“…The population structure determined using microsatellite data was initially analysed adopting three statistical approaches: the Bayesian methods implemented in the programme BAPS 4.14 (Corander et al, 2003(Corander et al, , 2004 and STRUCTURE 2.2 (Pritchard et al, 2000;Falush et al, 2003Falush et al, , 2007, and Genetic Landscape Shape analysis (Miller, 2005). The population structure based on mt data has been presented by Tollefsrud et al (2008b); here, we only performed Genetic Landscape Shape analysis of the mtDNA data to facilitate direct comparison between the geographical patterns of differentiation observed between the two marker types.…”

Section: Population Genetic Structurementioning

confidence: 99%

Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies

et al. 2009

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Norway spruce of northern Europe expanded at the end of the last glacial out of one refugium in Russia. To provide a detailed insight into how the genetic structure in the northern European lineage of this species has been shaped by postglacial migration, recurrent pollen flow and marginality, we here compare variation at seven highly variable nuclear microsatellite loci in 37 populations (1715 trees) with mitochondrial DNA variation. Microsatellite diversity was high (H E ¼ 0.640) and genetic differentiation was low (F ST ¼ 0.029). The microsatellite structure supported a mitochondrial DNA (mtDNA)-based hypothesis of two migration routes out of a single Russian refugium; one northwestern over Finland to northern Scandinavia, and one southwestern across the Baltic Sea into southern Scandinavia. Microsatellite diversity was maintained along the southwestern migration routes, whereas a significant decrease was observed towards the north. In contrast, the mtDNA diversity suggested higher amounts of historical gene flow towards the north than along the southwestern migration route. This suggests that the loss of nuclear diversity after postglacial colonization has been efficiently replenished by pollen-mediated gene flow in the south. Towards the north, smaller effective population size because of more limited seed and pollen production may have caused decreased nuclear diversity and increased inbreeding, reflecting the ecological marginality of the species in the north.

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BAPS 2: enhanced possibilities for the analysis of genetic population structure

Abstract: Freely available at http://www.rni.helsinki.fi/~jic/bapspage.html.

Cited by 429 publications

References 24 publications

Ecological Zones Rather Than Molecular Forms Predict Genetic Differentiation in the Malaria VectorAnopheles gambiaes.s. in Ghana

Ecological Zones Rather Than Molecular Forms Predict Genetic Differentiation in the Malaria VectorAnopheles gambiaes.s. in Ghana

Effective population size is strongly correlated with breeding pond size in the endangered California tiger salamander, Ambystoma californiense

Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies

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