<scp>smogd</scp>: software for the measurement of genetic diversity

Crawford, Nicholas G.

doi:10.1111/j.1755-0998.2009.02801.x

Cited by 564 publications

(419 citation statements)

References 19 publications

Supporting

Mentioning

415

Contrasting

Unclassified

Order By: Relevance

“…The excluding null allele (ENA) method in FreeNA (Chapuis & Estoup, 2007) was used to calculate pairwise F ST to avoid potential bias induced by null alleles. As a complementary estimate of genetic differentiation, we computed the Jost's D statistic (Jost, 2008) with the SMOGD software (Crawford, 2010). …”

Section: Methodsmentioning

confidence: 99%

Contrasted levels of genetic diversity in a benthic Mediterranean octocoral: Consequences of different demographic histories?

Masmoudi

Chaoui

Topçu

et al. 2016

Ecology and Evolution

View full text Add to dashboard Cite

Understanding the factors explaining the observed patterns of genetic diversity is an important question in evolutionary biology. We provide the first data on the genetic structure of a Mediterranean octocoral, the yellow gorgonian Eunicella cavolini, along with insights into the demographic history of this species. We sampled populations in four areas of the Mediterranean Sea: continental France, Algeria, Turkey, and the Balearic and Corsica islands. Along French coasts, three sites were sampled at two depths (20 and 40 m). We demonstrated a high genetic structure in this species (overall FST = 0.13), and most pairwise differentiation tests were significant. We did not detect any difference between depths at the same site. Clustering analyses revealed four differentiated groups corresponding to the main geographical areas. The levels of allelic richness and heterozygosity were significantly different between regions, with highest diversity in Algeria and lowest levels in Turkey. The highest levels of private allelic richness were observed in Algeria followed by Turkey. Such contrasted patterns of genetic diversity were not observed in other Mediterranean octocorals and could be the result of different evolutionary histories. We also provide new empirical evidence of contrasting results between tests and model‐based studies of demographic history. Our results have important consequences for the management of this species.

show abstract

Section: Methodsmentioning

confidence: 99%

Contrasted levels of genetic diversity in a benthic Mediterranean octocoral: Consequences of different demographic histories?

Masmoudi

Chaoui

Topçu

et al. 2016

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…Multilocus D is calculated as described by (Crawford 2010), and multilocus

G_{ST}

is calculated as proposed in (Nei 1973). …”

Section: Theorymentioning

confidence: 99%

Directional genetic differentiation and relative migration

Sundqvist

Keenan

Zackrisson

et al. 2016

Ecology and Evolution

244

223

View full text Add to dashboard Cite

Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly used to gather this information. One potential caveat is that these measures assume gene flow to be symmetric. However, asymmetric gene flow is common in nature, especially in systems driven by physical processes such as wind or water currents. As information about levels of asymmetric gene flow among populations is essential for the correct interpretation of the distribution of contemporary genetic diversity within species, this should not be overlooked. To obtain information on asymmetric migration patterns from genetic data, complex models based on maximum‐likelihood or Bayesian approaches generally need to be employed, often at great computational cost. Here, a new simpler and more efficient approach for understanding gene flow patterns is presented. This approach allows the estimation of directional components of genetic divergence between pairs of populations at low computational effort, using any of the classical or modern measures of genetic differentiation. These directional measures of genetic differentiation can further be used to calculate directional relative migration and to detect asymmetries in gene flow patterns. This can be done in a user‐friendly web application called divMigrate‐online introduced in this study. Using simulated data sets with known gene flow regimes, we demonstrate that the method is capable of resolving complex migration patterns under a range of study designs.

show abstract

“…The diversity within (∆ S /∆ T ) and between (∆ ST ) subpopulations, the relative population differentiation (D) and Jost"s haploid estimate of D (D est(hap) ) (Jost, 2008) were determined with SMOGD 1.2.5 (Crawford, 2010). D est is calculated from population estimates that incorporate sample size and ploidy, where a diploid genome is assumed.…”

Section: Genetic Diversity Of the K Proteae Population And Origin Ofmentioning

confidence: 99%

“…Human activity and movement of plant materials is also commonly implicated in the dispersal of fungi and has resulted in the spread of devastating pathogens between countries and continents (Brown & Hovmøller, 2002;Wingfield et al, 2001;2010). Examples of migration at an intercontinental or even global scale are available for lichen-forming (Buschbom, 2007), saprobic (Moncalvo & Buchanan, 2008), ectomycorrhizal (Moyersoen et al, 2003) and marine fungi (Pang et al, 2013).…”

Section: Long-distance Dispersal Between Distant K Proteae Populationsmentioning

confidence: 99%

Long-distance dispersal and recolonization of a fire-destroyed niche by a mite-associated fungus

et al. 2015

View full text Add to dashboard Cite

The Fynbos Biome in the Core Cape Subregion of South Africa is prone to recurrent fires that can clear vast areas of vegetation. Between periods of fire, ophiostomatoid fungi colonize the fruiting structures of serotinous Protea species through arthropod-mediated dispersal. Using microsatellite markers, this study considered the process whereby a Protea-associated ophiostomatoid fungus, Knoxdaviesia proteae, recolonizes a burnt area. The genetic diversity, composition and structure of fungal populations from young P. repens plants in a recently burnt area were compared to populations from the adjacent, unburnt Protea population. The only difference between K. proteae populations from the two areas was found in the number of private alleles, which was significantly higher in the unburnt population. The population structure, although weak, indicated that most K. proteae 1 individuals from recently burnt areas originated from the unburnt population. However, individuals from unsampled source populations were also detected. This, together with the lack of isolation-by-distance across the landscape, suggested that long-distance dispersal is important for K. proteae to recolonize burnt areas. Similarly, the high level of gene flow and low differentiation observed between two distantly separated K. proteae populations also supported the existence of long-distance dispersal. The genetic cohesiveness of populations over long distances and the genetic diversity within populations could be attributed to frequent multiple fungal migration events mediated primarily by arthropods but, potentially, also by birds.

show abstract

smogd: software for the measurement of genetic diversity

Cited by 564 publications

References 19 publications

Contrasted levels of genetic diversity in a benthic Mediterranean octocoral: Consequences of different demographic histories?

Contrasted levels of genetic diversity in a benthic Mediterranean octocoral: Consequences of different demographic histories?

Directional genetic differentiation and relative migration

Long-distance dispersal and recolonization of a fire-destroyed niche by a mite-associated fungus

Contact Info

Product

Resources

About