scholarly journals Selective sweeps under dominance and inbreeding

2018 ◽  
Author(s):  
Matthew Hartfield ◽  
Thomas Bataillon
Keyword(s):  
Positive Selection ◽  
De Novo ◽  
Evolutionary Genetics ◽  
Recurrent Mutation ◽  
Selective Sweeps ◽  
Major Research ◽  
Standing Variation ◽  
Research Goal ◽  
Beneficial Allele ◽  
Novel Allele

AbstractA major research goal in evolutionary genetics is to uncover loci experiencing positive selection. One approach involves finding ‘selective sweeps’ patterns, which can either be ‘hard sweeps’ formed by de novo mutation, or ‘soft sweeps’ arising from recurrent mutation or existing standing variation. Existing theory generally assumes outcrossing populations, and it is unclear how dominance affects soft sweeps. We consider how arbitrary dominance and inbreeding via self-fertilisation affect hard and soft sweep signatures. With increased self-fertilisation, they are maintained over longer map distances due to reduced effective recombination and faster beneficial allele fixation times. Dominance can affect sweep patterns in outcrossers if the derived variant originates from either a single novel allele, or from recurrent mutation. These models highlight the challenges in distinguishing hard and soft sweeps, and propose methods to differentiate between scenarios.

scholarly journals Selective Sweeps Under Dominance and Inbreeding

2020 ◽  
Vol 10 (3) ◽  
pp. 1063-1075 ◽  
Author(s):  
Matthew Hartfield ◽  
Thomas Bataillon
Keyword(s):  
De Novo ◽  
Evolutionary Genetics ◽  
Recurrent Mutation ◽  
Selective Sweeps ◽  
Major Research ◽  
Standing Variation ◽  
Self Fertilization ◽  
Research Goal ◽  
Beneficial Allele ◽  
Novel Allele

A major research goal in evolutionary genetics is to uncover loci experiencing positive selection. One approach involves finding ‘selective sweeps’ patterns, which can either be ‘hard sweeps’ formed by de novo mutation, or ‘soft sweeps’ arising from recurrent mutation or existing standing variation. Existing theory generally assumes outcrossing populations, and it is unclear how dominance affects soft sweeps. We consider how arbitrary dominance and inbreeding via self-fertilization affect hard and soft sweep signatures. With increased self-fertilization, they are maintained over longer map distances due to reduced effective recombination and faster beneficial allele fixation times. Dominance can affect sweep patterns in outcrossers if the derived variant originates from either a single novel allele, or from recurrent mutation. These models highlight the challenges in distinguishing hard and soft sweeps, and propose methods to differentiate between scenarios.

scholarly journals Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation

PLoS Genetics ◽  
2012 ◽  
Vol 8 (10) ◽  
pp. e1003011 ◽  
Author(s):  
Benjamin M. Peter ◽  
Emilia Huerta-Sanchez ◽  
Rasmus Nielsen
Keyword(s):  
De Novo ◽  
De Novo Mutation ◽  
Selective Sweeps ◽  
Standing Variation

scholarly journals De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa

2021 ◽  
Author(s):  
Magdalena Bohutínská ◽  
Vinzenz Handrick ◽  
Levi Yant ◽  
Roswitha Schmickl ◽  
Filip Kolář ◽  
...  
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
De Novo ◽  
Empirical Studies ◽  
De Novo Mutation ◽  
Rapid Adaptation ◽  
De Novo Mutations ◽  
Standing Variation ◽  
Arabidopsis Arenosa ◽  
Meiosis Genes

Abstract A sudden shift in environment or cellular context necessitates rapid adaptation. A dramatic example is genome duplication, which leads to polyploidy. In such situations, the waiting time for new mutations might be prohibitive; theoretical and empirical studies suggest that rapid adaptation will largely rely on standing variation already present in source populations. Here, we investigate the evolution of meiosis proteins in Arabidopsis arenosa, some of which were previously implicated in adaptation to polyploidy, and in a diploid, habitat. A striking and unexplained feature of prior results was the large number of amino acid changes in multiple interacting proteins, especially in the relatively young tetraploid. Here, we investigate whether selection on meiosis genes is found in other lineages, how the polyploid may have accumulated so many differences, and whether derived variants were selected from standing variation. We use a range-wide sample of 145 resequenced genomes of diploid and tetraploid A. arenosa, with new genome assemblies. We confirmed signals of positive selection in the polyploid and diploid lineages they were previously reported in and find additional meiosis genes with evidence of selection. We show that the polyploid lineage stands out both qualitatively and quantitatively. Compared with diploids, meiosis proteins in the polyploid have more amino acid changes and a higher proportion affecting more strongly conserved sites. We find evidence that in tetraploids, positive selection may have commonly acted on de novo mutations. Several tests provide hints that coevolution, and in some cases, multinucleotide mutations, might contribute to rapid accumulation of changes in meiotic proteins.

An intronic variant disrupts mRNA splicing and causes FGFR3-related skeletal dysplasia

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Ting Xu ◽  
Liang Shi ◽  
Weiqian Dai ◽  
Xuefan Gu ◽  
Yongguo Yu ◽  
...  
Keyword(s):  
De Novo ◽  
Clinical Findings ◽  
Recurrent Mutation ◽  
Mrna Splicing ◽  
Additional Patient ◽  
Missense Mutations ◽  
Splicing Variant ◽  
Amino Acid Insertion ◽  
Whole Exome ◽  
Minigene Assay

Abstract Objectives Achondroplasia and hypochondroplasia are the most common forms of disproportionate short stature, of which the vast majority of cases can be attributed to the hotspot missense mutations in the gene FGFR3. Here we presented cases with a novel cryptic splicing variant of FGFR3 gene and aimed to interrogate the variant pathogenicity. Case presentaiton In whole exome sequencing of two patients with hypochondroplasia-like features, a de novo intronic variant c.1075 + 95C>G was identified, predicted to alter mRNA splicing. Minigene assay showed that this intronic variant caused retention of a 90-nucleotide segment of intron 8 in mRNA, resulting in a 30-amino acid insertion at the extracellular domain of the protein. This is the first likely pathogenic splicing variant identified in the FGFR3 gene and was detected in one additional patient among 26 genetically unresolved patients. Conclustions Our results strongly suggest that c.1075 + 95C>G is a recurrent mutation and should be included in genetic testing of FGFR3 especially for those patients with equivocal clinical findings and no exonic mutations identified.

scholarly journals Eliciting probabilistic expectations: Collaborations between psychologists and economists

2017 ◽  
Vol 114 (13) ◽  
pp. 3297-3304 ◽  
Author(s):  
Wändi Bruine de Bruin ◽  
Baruch Fischhoff
Keyword(s):  
Common Ground ◽  
Research Process ◽  
Economic Modeling ◽  
Common Language ◽  
Mutual Benefit ◽  
Purchasing Decisions ◽  
Major Research ◽  
Sense Of Ownership ◽  
Research Goal ◽  
Essential Support

We describe two collaborations in which psychologists and economists provided essential support on foundational projects in major research programs. One project involved eliciting adolescents’ expectations regarding significant future life events affecting their psychological and economic development. The second project involved eliciting consumers’ expectations regarding inflation, a potentially vital input to their investment, saving, and purchasing decisions. In each project, we sought questions with the precision needed for economic modeling and the simplicity needed for lay respondents. We identify four conditions that, we believe, promoted our ability to sustain these transdisciplinary collaborations and coproduce the research: (i) having a shared research goal, which neither discipline could achieve on its own; (ii) finding common ground in shared methodology, which met each discipline’s essential evidentiary conditions, but without insisting on its culturally acquired tastes; (iii) sharing the effort throughout, with common language and sense of ownership; and (iv) gaining mutual benefit from both the research process and its products.

scholarly journals Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus

2021 ◽  
Author(s):  
Julia M. Kreiner ◽  
Amalia Caballero ◽  
Stephen I. Wright ◽  
John R. Stinchcombe
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Sex Differentiation ◽  
Common Garden ◽  
Whole Genome Sequence ◽  
Secondary Contact ◽  
Natural Environments ◽  
Relative Role ◽  
Standing Variation ◽  
Amaranthus Tuberculatus

The relative role of hybridization, de novo evolution, and standing variation in weed adaptation to agricultural environments is largely unknown. In Amaranthus tuberculatus, a widespread North American agricultural weed, adaptation is likely influenced by recent secondary contact and admixture of two previously isolated subspecies. We characterized the extent of adaptation and phenotypic differentiation accompanying the spread of A. tuberculatus into agricultural environments and the contribution of subspecies divergence. We generated phenotypic and whole-genome sequence data from a manipulative common garden experiment, using paired samples from natural and agricultural populations. We found strong latitudinal, longitudinal, and sex differentiation in phenotypes, and subtle differences among agricultural and natural environments that were further resolved with ancestry-based inference. The transition into agricultural environments has favoured southwestern var. rudis ancestry that leads to higher biomass and environment-specific phenotypes: increased biomass and earlier flowering under reduced water availability, and reduced plasticity in fitness-related traits. We also detected de novo adaptation to agricultural habitats independent of ancestry effects, including marginally higher biomass and later flowering in agricultural populations, and a time to germination home advantage. Therefore, the invasion of A. tuberculatus into agricultural environments has drawn on adaptive variation across multiple timescales—through both preadaptation via the preferential sorting of var. rudis ancestry and de novo local adaptation.

scholarly journals Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

2021 ◽  
Author(s):  
Ching-Ho Chang ◽  
Lauren E. Gregory ◽  
Kathleen E. Gordon ◽  
Colin D. Meiklejohn ◽  
Amanda M. Larracuente
Keyword(s):  
Positive Selection ◽  
Y Chromosome ◽  
Related Species ◽  
De Novo ◽  
Gene Families ◽  
Chromosome Organization ◽  
End Joining ◽  
Sexual Antagonism ◽  
Closely Related Species ◽  
Y Chromosomes

AbstractY chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposable elements, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism generally contributes to the convergent evolution of Y chromosome organization.

scholarly journals Major stages of vertebrate adaptive radiation are assembled from a disparate spatiotemporal landscape

2020 ◽  
Author(s):  
Emilie J. Richards ◽  
Joseph A. McGirr ◽  
Jeremy R. Wang ◽  
Michelle E. St. John ◽  
Jelmer W. Poelstra ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Genetic Variants ◽  
De Novo ◽  
Craniofacial Development ◽  
Standing Variation ◽  
Three Stages ◽  
The Caribbean ◽  
Selection For ◽  
Trophic Niches ◽  
Clear Support

AbstractTo investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of genetic variants underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. Ancient standing variation from disparate spatial sources was reassembled into new combinations which are under strong selection for adaptation to novel trophic niches on only a single island throughout the Caribbean. This occurred in three stages: first, standing variation associated with feeding behavior swept, then standing variation regulating craniofacial development and pigmentation, and finally de novo variation for craniofacial development. Our results provide clear support for two longstanding hypotheses about adaptive radiation and demonstrate how ancient alleles maintained for millennia in distinct environmental refugia can be assembled into new adaptive combinations.One Sentence SummaryAncient origins of adaptive radiation

scholarly journals The Genomic Architecture of a Rapid Island Radiation: Recombination Rate Variation, Chromosome Structure, and Genome Assembly of the Hawaiian Cricket Laupala

2017 ◽  
Author(s):  
Thomas Blankers ◽  
Kevin P. Oh ◽  
Aureliano Bombarely ◽  
Kerry L. Shaw
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Evolutionary Genetics ◽  
Rate Variation ◽  
Linkage Maps ◽  
Recombination Rates ◽  
Behavioral Isolation ◽  
Genomic Architecture ◽  
Suppressed Recombination

ABSTRACTPhenotypic evolution and speciation depend on recombination in many ways. Within populations, recombination can promote adaptation by bringing together favorable mutations and decoupling beneficial and deleterious alleles. As populations diverge, cross-over can give rise to maladapted recombinants and impede or reverse diversification. Suppressed recombination due to genomic rearrangements, modifier alleles, and intrinsic chromosomal properties may offer a shield against maladaptive gene flow eroding co-adapted gene complexes. Both theoretical and empirical results support this relationship. However, little is known about this relationship in the context of behavioral isolation, where co-evolving signals and preferences are the major hybridization barrier. Here we examine the genomic architecture of recently diverged, sexually isolated Hawaiian swordtail crickets (Laupala). We assemble a de novo genome and generate three dense linkage maps from interspecies crosses. In line with expectations based on the species’ recent divergence and successful interbreeding in the lab, the linkage maps are highly collinear and show no evidence for large-scale chromosomal rearrangements. The maps were then used to anchor the assembly to pseudomolecules and estimate recombination rates across the genome. We tested the hypothesis that loci involved in behavioral isolation (song and preference divergence) are in regions of low interspecific recombination. Contrary to our expectations, a genomic region where a male song QTL co-localizes with a female preference QTL was not associated with particularly low recombination rates. This study provides important novel genomic resources for an emerging evolutionary genetics model system and suggests that trait-preference co-evolution is not necessarily facilitated by locally suppressed recombination.

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