Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

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Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

10.1101/819219 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jing Wang ◽

Nathaniel R. Street ◽

Eung-Jun Park ◽

Jianquan Liu ◽

Pär K. Ingvarsson

Keyword(s):

Recurrent Selection ◽

Balancing Selection ◽

Forest Tree ◽

Species Variation ◽

Recombination Rates ◽

Genome Wide ◽

Genomic Landscape ◽

Speciation Continuum ◽

Whole Genome Resequencing

AbstractIncreasing our understanding of how various evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, the genome-wide patterns of within- and between-species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories, investigate patterns of diversity and divergence, infer their genealogical relationships and estimate the extent of ancient introgression across the genome. Our results show substantial variation in these patterns along the genomes although this variation is not randomly distributed but is strongly predicted by the local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection are also crucial components in shaping patterns of genome-wide variation during the speciation process.

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Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching

Science ◽

10.1126/science.aba4674 ◽

2020 ◽

Vol 369 (6501) ◽

pp. eaba4674 ◽

Cited By ~ 14

Author(s):

Zachary L. Fuller ◽

Veronique J. L. Mocellin ◽

Luke A. Morris ◽

Neal Cantin ◽

Jihanne Shepherd ◽

...

Keyword(s):

Genome Wide Association Study ◽

Balancing Selection ◽

Conservation Strategies ◽

Genome Sequences ◽

Acropora Millepora ◽

Genome Wide ◽

A Genome ◽

Bleaching Response ◽

In The Wild

Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.

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Signatures of long-term balancing selection in human genomes

10.1101/119529 ◽

2017 ◽

Cited By ~ 2

Author(s):

Bárbara Domingues Bitarello ◽

Cesare de Filippo ◽

João Carlos Teixeira ◽

Joshua M. Schmidt ◽

Philip Kleinert ◽

...

Keyword(s):

Balancing Selection ◽

Theoretical Perspective ◽

Human Populations ◽

Protein Coding ◽

Human Genomes ◽

Genome Wide ◽

Higher Power ◽

Genome Wide Data ◽

Immune Related Genes

AbstractBalancing selection maintains advantageous diversity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe the Non-Central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: about 0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (p < 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap about 8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.

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Viability, behaviour, and colour expression in the offspring of matings between common wall lizard Podarcis muralis colour morphs

Current Zoology ◽

10.1093/cz/zoab039 ◽

2021 ◽

Author(s):

Javier Abalos ◽

Guillem Pérez i de Lanuza ◽

Alicia Bartolomé ◽

Fabien Aubret ◽

Tobias Uller ◽

...

Keyword(s):

Reproductive Output ◽

Balancing Selection ◽

Phenotypic Variability ◽

Investment Strategies ◽

Podarcis Muralis ◽

Common Wall ◽

Genome Wide ◽

Colour Morphs ◽

Embryonic Viability

Abstract Colour polymorphisms are widely studied to identify the mechanisms responsible for the origin and maintenance of phenotypic variability in nature. Two of the mechanisms of balancing selection currently thought to explain the long-term persistence of polymorphisms are the evolution of alternative phenotypic optima through correlational selection on suites of traits including colour, and heterosis. Both of these mechanisms can generate differences in offspring viability and fitness arising from different morph combinations. Here, we examined the effect of parental morph combination on fertilisation success, embryonic viability, newborn quality, antipredator and foraging behaviour, as well as inter-annual survival by conducting controlled matings in a polymorphic lacertid Podarcis muralis, where colour morphs are frequently assumed to reflect alternative phenotypic optima (e.g. alternative reproductive strategies). Juveniles were kept in outdoor tubs for a year in order to study inter-annual growth, survival, and morph inheritance. In agreement with a previous genome-wide association analysis, morph frequencies in the year-old juveniles matched the frequencies expected if orange and yellow expression depended on recessive homozygosity at two separate loci. Our findings also agree with previous literature reporting higher reproductive output of heavy females and the higher overall viability of heavy newborn lizards, but we found no evidence for the existence of alternative breeding investment strategies in female morphs, or morph-combination effects on offspring viability and behaviour. We conclude that inter-morph breeding remains entirely viable and genetic incompatibilities are of little significance for the maintenance of discrete colour morphs in P. muralis from the Pyrenees.

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