Genomic insights into positive selection

Biswas, Shameek; Akey, Joshua M.

doi:10.1016/j.tig.2006.06.005

Cited by 415 publications

(336 citation statements)

References 62 publications

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“…Some intervals of Tajima's D for the AS population are >1, which may be caused by the balancing selection for diverse allele content; this is congruent with the genetic diversity comparison, which shows significantly higher genetic diversity in the AS population (30). The fact that Tajima's D value < −4 was only in the ES population indicates that this population is under stronger positive selection or that the population is expanding (30).…”

Section: Resultssupporting

confidence: 71%

Sympatric speciation of spiny mice, Acomys , unfolded transcriptomically at Evolution Canyon, Israel

Wang

Cai

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Spiny mice, Acomys cahirinus, colonized Israel 30,000 y ago from dry tropical Africa and inhabited rocky habitats across Israel. Earlier, we had shown by mtDNA that A. cahirinus incipiently sympatrically speciates at Evolution Canyon I (EC I) in Mount Carmel, Israel because of microclimatic interslope divergence. The EC I microsite consists of a dry and hot savannoid "African" slope (AS) and an abutting humid and cool-forested "European" slope (ES). Here, we substantiate incipient SS in A. cahirinus at EC I based on the entire transcriptome, showing that multiple slope-specific adaptive complexes across the transcriptome result in two divergent clusters. Tajima's D distribution of the abutting Acomys interslope populations shows that the ES population is under stronger positive selection, whereas the AS population is under balancing selection, harboring higher genetic polymorphisms. Considerable sites of the two populations were differentiated with a coefficient of F ST = 0.25-0.75. Remarkably, 24 and 37 putatively adaptively selected genes were detected in the AS and ES populations, respectively. The AS genes involved DNA repair, growth arrest, neural cell differentiation, and heat-shock proteins adapting to the local AS stresses of high solar radiation, drought, and high temperature. In contrast, the ES genes involved high ATP associated with energetics stress. The sharp ecological interslope divergence led to strong slope-specific selection overruling the interslope gene flow. Earlier tests suggested slope-specific mate choice. Habitat interslope-adaptive selection across the transcriptome and mate choice substantiate sympatric speciation (SS), suggesting its prevalence at EC I and commonality in nature.adaptive ecological speciation | microclimate | natural selection | RNA-seq

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Section: Resultssupporting

confidence: 71%

Sympatric speciation of spiny mice, Acomys , unfolded transcriptomically at Evolution Canyon, Israel

Wang

Cai

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…The positive Tajima's D values in both genes indicate a trend toward excess of intermediate frequency alleles. This effect can be caused by population bottlenecks, structure, or balancing selection (Biswas and Akey 2006). In view of the strong evidence for significant population structure in the plant material used here, this may be a contributing factor.…”

Section: Discussionmentioning

confidence: 92%

Association of Candidate Genes With Flowering Time and Water-Soluble Carbohydrate Content in Lolium perenne (L.)

Skøt

Humphreys

et al. 2007

Genetics

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We describe a candidate gene approach for associating SNPs with variation in flowering time and watersoluble carbohydrate (WSC) content and other quality traits in the temperate forage grass species Lolium perenne. Three analysis methods were used, which took the significant population structure into account. First, a linear mixed model was used enabling a structured association analysis to be incorporated with the nine populations identified in the structure analysis as random variables. Second, a within-population analysis of variance was performed. Third, a tree-scanning method was used, in which haplotype trees were associated with phenotypes on the basis of inferred haplotypes. Analysis of variance within populations identified several associations between WSC, nitrogen (N), and dry matter digestibility with allelic variants within an alkaline invertase candidate gene LpcAI. These associations were only detected in material harvested in one of the two years. By contrast, consistent associations between the L. perenne homolog (LpHD1) of the rice photoperiod control gene HD1 and flowering time were identified. One SNP, in the immediate upstream region of the LpHD1 coding sequence (C-4443-A), was significant in the linear mixed model. Within-population analysis of variance and tree-scanning analysis confirmed and extended this result to the 2118 polymorphisms in some of the populations. The merits of the tree-scanning method are compared to the single SNP analysis. The potential usefulness of the 4443 SNP in marker-assisted selection is currently being evaluated in test crosses of genotypes from this work with turf-grass varieties.

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“…In addition, assessment of hybridization frequencies and comprehensive tests for introgression are precluded from these studies because DNA pools were used (21,23,27), sample sizes were too small (24,26), or such assessments may be irrelevant because M and S laboratory colony mosquitoes were used (28). Finally, there are strong limitations in relying on genome scans alone for detecting selection, gene flow, and recombination that occurs during speciation (33,34).…”

Section: Significancementioning

confidence: 99%

Spatiotemporal dynamics of gene flow and hybrid fitness between the M and S forms of the malaria mosquito, Anopheles gambiae

Marsden²,

Norris

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

103

171

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The M and S forms of Anopheles gambiae have been the focus of intense study by malaria researchers and evolutionary biologists interested in ecological speciation. Divergence occurs at three discrete islands in genomes that are otherwise nearly identical. An "islands of speciation" model proposes that diverged regions contain genes that are maintained by selection in the face of gene flow. An alternative "incidental island" model maintains that gene flow between M and S is effectively zero and that divergence islands are unrelated to speciation. A "divergence island SNP" assay was used to explore the spatial and temporal distributions of hybrid genotypes. Results revealed that hybrid individuals occur at frequencies ranging between 5% and 97% in every population examined. A temporal analysis revealed that assortative mating is unstable and periodically breaks down, resulting in extensive hybridization. Results suggest that hybrids suffer a fitness disadvantage, but at least some hybrid genotypes are viable. Stable introgression of the 2L speciation island occurred at one site following a hybridization event.reproductive isolation | population structure | Anopheles coluzzii

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Genomic insights into positive selection

Cited by 415 publications

References 62 publications

Sympatric speciation of spiny mice, Acomys , unfolded transcriptomically at Evolution Canyon, Israel

Sympatric speciation of spiny mice, Acomys , unfolded transcriptomically at Evolution Canyon, Israel

Association of Candidate Genes With Flowering Time and Water-Soluble Carbohydrate Content in Lolium perenne (L.)

Spatiotemporal dynamics of gene flow and hybrid fitness between the M and S forms of the malaria mosquito, Anopheles gambiae

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