LOSITAN: A workbench to detect molecular adaptation based on a F st -outlier method

Antão, Tiago; Lopes, Ana Lúcia; Lopes, Ricardo; Beja‐Pereira, Albano; Luikart, Gordon

doi:10.1186/1471-2105-9-323

Cited by 1,022 publications

(938 citation statements)

References 12 publications

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“…We tested for evidence of selection using a coalescent‐based approach (Beaumont & Nichols, 1996) implemented in LOSITAN (Antao, Lopes, Lopes, Beja‐Pereira, & Luikart, 2008), a software platform used to detect signatures of selection based on the distribution of F ST as a function of heterozygosity. We calculated the “neutral” mean F ST , where we first ran a simulation to remove potentially selected loci prior to computing the initial mean F ST , upon which putative adaptive loci were identified.…”

Section: Methodsmentioning

confidence: 99%

Signatures of selection in mammalian clock genes with coding trinucleotide repeats: Implications for studying the genomics of high‐pace adaptation

Prentice

Bowman

Lalor

et al. 2017

Ecology and Evolution

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Climate change is predicted to affect the reproductive ecology of wildlife; however, we have yet to understand if and how species can adapt to the rapid pace of change. Clock genes are functional genes likely critical for adaptation to shifting seasonal conditions through shifts in timing cues. Many of these genes contain coding trinucleotide repeats, which offer the potential for higher rates of change than single nucleotide polymorphisms (SNPs) at coding sites, and, thus, may translate to faster rates of adaptation in changing environments. We characterized repeats in 22 clock genes across all annotated mammal species and evaluated the potential for selection on repeat motifs in three clock genes (NR1D1,CLOCK, and PER1) in three congeneric species pairs with different latitudinal range limits: Canada lynx and bobcat (Lynx canadensis and L. rufus), northern and southern flying squirrels (Glaucomys sabrinus and G. volans), and white‐footed and deer mouse (Peromyscus leucopus and P. maniculatus). Signatures of positive selection were found in both the interspecific comparison of Canada lynx and bobcat, and intraspecific analyses in Canada lynx. Northern and southern flying squirrels showed differing frequencies at common CLOCK alleles and a signature of balancing selection. Regional excess homozygosity was found in the deer mouse at PER1 suggesting disruptive selection, and further analyses suggested balancing selection in the white‐footed mouse. These preliminary signatures of selection and the presence of trinucleotide repeats within many clock genes warrant further consideration of the importance of candidate gene motifs for adaptation to climate change.

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Section: Methodsmentioning

confidence: 99%

Signatures of selection in mammalian clock genes with coding trinucleotide repeats: Implications for studying the genomics of high‐pace adaptation

Prentice

Bowman

Lalor

et al. 2017

Ecology and Evolution

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“…BAYESCAN outcomes were plotted using the R functions provided by the program. The FDIST F ST method implemented in the LOSITAN software (Antao, Lopes, Lopes, Beja‐Pereira, & Luikart, 2008) was used to investigate loss of heterozygosity (expected after selective sweeps) regarding F ST . For this program, a total of 100,000 simulations, a population size of 50, and the infinite allele mutation model were used.…”

Section: Methodsmentioning

confidence: 99%

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Prado

Vera

Hermida

et al. 2018

Evolutionary Applications

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Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double‐digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.

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“…Outlier loci were assessed based on the relationship between F ST and expected heterozygosity ( H E ) according to an island model with neutral markers (Beaumont & Nichols, 1996), using the program LOSITAN (Antao, Lopes, Lopes, Beja‐Pereira, & Luikart, 2008). This method assumes that loci with F ST excessively high or low, compared to the expectations under neutrality conditions, are candidates to be under selection (Antao et al., 2008; Schoville et al., 2012).…”

Section: Methodsmentioning

confidence: 99%

“…This method assumes that loci with F ST excessively high or low, compared to the expectations under neutrality conditions, are candidates to be under selection (Antao et al., 2008; Schoville et al., 2012). LOSITAN was run in pairs, considering three scenarios: Semideciduous Forest versus Rainforest, Semideciduous Forest versus Restinga Forest, and Rainforest versus Restinga Forest, using the parameter setting of 100,000 simulations, confident interval of 0.95, and false discovery rate (FDR) of 0.1.…”

Section: Methodsmentioning

confidence: 99%

Phenotypic plasticity and local adaptation favor range expansion of a Neotropical palm

Brancalion

Oliveira

Zucchi

et al. 2018

Ecology and Evolution

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One of the most intriguing questions in plant ecology is which evolutionary strategy allows widely distributed species to increase their ecological range and grow in changing environmental conditions. Phenotypic plasticity and local adaptations are major processes governing species range margins, but little is known about their relative contribution for tree species distribution in tropical forest regions. We investigated the relative role of phenotypic plasticity and local adaptation in the ecological distribution of the widespread palm Euterpe edulis in the Brazilian Atlantic Forest. Genetic sampling and experiments were performed in old‐growth remnants of two forest types with higher (Seasonal Semideciduous Forests vs. Submontane Rainforest) and lower biogeographic association and environmental similarities (Submontane Rainforest vs. Restinga Forest). We first assessed the molecular genetic differentiation among populations, focusing on the group of loci potentially under selection in each forest, using single‐nucleotide polymorphism (SNPs) outliers. Further, we looked for potential adaptive divergence among populations in a common garden experiment and in reciprocal transplants for two plant development phases: seedling establishment and sapling growth. Analysis with outlier loci indicated that all individuals from the Semideciduous Forest formed a single group, while another group was formed by overlapping individuals from Submontane Rainforest and Restinga Forest. Molecular differentiation was corroborated by reciprocal transplants, which yielded strong evidence of local adaptations for seedling establishment in the biogeographically divergent Rainforest and Semideciduous Forest, but not for Restinga Forest and Submontane Rainforest. Phenotypic plasticity for palm seedling establishment favors range expansion to biogeographically related or recently colonized forest types, while persistence in the newly colonized ecosystem may be favored by local adaptations if climatic conditions diverge over time, reducing gene flow between populations. SNPs obtained by next‐generation sequencing can help exploring adaptive genetic variation in tropical trees, which impose several challenges to the use of reciprocal transplants.

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LOSITAN: A workbench to detect molecular adaptation based on a F st -outlier method

Abstract: Background: Testing for selection is becoming one of the most important steps in the analysis of multilocus population genetics data sets. Existing applications are difficult to use, leaving many nontrivial, error-prone tasks to the user.

Cited by 1,022 publications

References 12 publications

Signatures of selection in mammalian clock genes with coding trinucleotide repeats: Implications for studying the genomics of high‐pace adaptation

Signatures of selection in mammalian clock genes with coding trinucleotide repeats: Implications for studying the genomics of high‐pace adaptation

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Phenotypic plasticity and local adaptation favor range expansion of a Neotropical palm

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