scholarly journals Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

2018 ◽  
Author(s):  
Patrick Monnahan ◽  
Filip Kolář ◽  
Pierre Baduel ◽  
Christian Sailer ◽  
Jordan Koch ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Genome Duplication ◽  
Purifying Selection ◽  
Theoretical Work ◽  
Deleterious Mutations ◽  
Evolutionary Potential ◽  
Genomic Signatures ◽  
Population Genomic ◽  
Variable Species ◽  
Arabidopsis Arenosa

AbstractPloidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ∼300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find the impacts of polyploidy on population genomic processes are subtle yet pervasive, including reduced efficiency on linked and purifying selection as well as rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution, and interploidy introgression all conspire to shape the evolutionary potential of polyploids.

scholarly journals Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

2019 ◽  
Vol 3 (3) ◽  
pp. 457-468 ◽  
Author(s):  
Patrick Monnahan ◽  
Filip Kolář ◽  
Pierre Baduel ◽  
Christian Sailer ◽  
Jordan Koch ◽  
...  
Keyword(s):  
Genome Duplication ◽  
Population Genomic ◽  
Arabidopsis Arenosa

scholarly journals Interspecific introgression mediates adaptation to whole genome duplication

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Sarah Marburger ◽  
Patrick Monnahan ◽  
Paul J. Seear ◽  
Simon H. Martin ◽  
Jordan Koch ◽  
...  
Keyword(s):  
Gene Flow ◽  
Opposite Direction ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Levels Of Selection ◽  
Whole Genome ◽  
Interspecific Introgression ◽  
Population Genomic ◽  
Genomic Study ◽  
Arabidopsis Arenosa

AbstractAdaptive gene flow is a consequential phenomenon across all kingdoms. Although recognition is increasing, there is no study showing that bidirectional gene flow mediates adaptation at loci that manage core processes. We previously discovered concerted molecular changes among interacting members of the meiotic machinery controlling crossover number upon adaptation to whole-genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that adaptation to WGD has been mediated by adaptive gene flow between A. arenosa and A. lyrata. We find that A. lyrata underwent WGD more recently than A. arenosa, suggesting that pre-adapted alleles have rescued nascent A. lyrata, but we also detect gene flow in the opposite direction at functionally interacting loci under the most extreme levels of selection. These data indicate that bidirectional gene flow allowed for survival after WGD, and that the merger of these species is greater than the sum of their parts.

The Age of Nonsynonymous and Synonymous Mutations in Animal mtDNA and Implications for the Mildly Deleterious Theory

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 497-506 ◽  
Author(s):  
Rasmus Nielsen ◽  
Daniel M Weinreich
Keyword(s):  
Dna Sequences ◽  
Purifying Selection ◽  
Data Sets ◽  
Deleterious Mutations ◽  
Synonymous Mutations ◽  
Weak Evidence ◽  
Mitochondrial Data ◽  
The Mean ◽  
Excess Number ◽  
Neutral Mutations

Abstract McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.

Regions of Lower Crossing Over Harbor More Rare Variants in African Populations ofDrosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 657-665 ◽  
Author(s):  
Peter Andolfatto ◽  
Molly Przeworski
Keyword(s):  
Frequency Spectrum ◽  
Nucleotide Diversity ◽  
Rare Variants ◽  
Purifying Selection ◽  
Crossing Over ◽  
Background Selection ◽  
Deleterious Mutations ◽  
African Populations ◽  
Rapid Fixation ◽  
Parameter Values

AbstractA correlation between diversity levels and rates of recombination is predicted both by models of positive selection, such as hitchhiking associated with the rapid fixation of advantageous mutations, and by models of purifying selection against strongly deleterious mutations (commonly referred to as “background selection”). With parameter values appropriate for Drosophila populations, only the first class of models predicts a marked skew in the frequency spectrum of linked neutral variants, relative to a neutral model. Here, we consider 29 loci scattered throughout the Drosophila melanogaster genome. We show that, in African populations, a summary of the frequency spectrum of polymorphic mutations is positively correlated with the meiotic rate of crossing over. This pattern is demonstrated to be unlikely under a model of background selection. Models of weakly deleterious selection are not expected to produce both the observed correlation and the extent to which nucleotide diversity is reduced in regions of low (but nonzero) recombination. Thus, of existing models, hitchhiking due to the recurrent fixation of advantageous variants is the most plausible explanation for the data.

scholarly journals Spontaneous whole-genome duplication restores fertility in interspecific hybrids

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Guillaume Charron ◽  
Souhir Marsit ◽  
Mathieu Hénault ◽  
Hélène Martin ◽  
Christian R. Landry
Keyword(s):  
Interspecific Hybrids ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Mitotic Cell ◽  
Whole Genome ◽  
Evolutionary Potential ◽  
Relaxed Selection ◽  
Interspecies Hybrids ◽  
Established Species ◽  
Fertility Recovery

Abstract Interspecies hybrids often show some advantages over parents but also frequently suffer from reduced fertility, which can sometimes be overcome through sexual reproduction that sorts out genetic incompatibilities. Sex is however inefficient due to the low viability or fertility of hybrid offspring and thus limits their evolutionary potential. Mitotic cell division could be an alternative to fertility recovery in species such as fungi that can also propagate asexually. Here, to test this, we evolve in parallel and under relaxed selection more than 600 diploid yeast inter-specific hybrids that span from 100,000 to 15 M years of divergence. We find that hybrids can recover fertility spontaneously and rapidly through whole-genome duplication. These events occur in both hybrids between young and well-established species. Our results show that the instability of ploidy in hybrid is an accessible path to spontaneous fertility recovery.

scholarly journals Transition from background selection to associative overdominance promotes diversity in regions of low recombination

2019 ◽  
Author(s):  
Kimberly J. Gilbert ◽  
Fanny Pouyet ◽  
Laurent Excoffier ◽  
Stephan Peischl
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Purifying Selection ◽  
Heterozygote Advantage ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Recombination Rates ◽  
Locus Model ◽  
Genome Wide ◽  
Linked Selection

SummaryLinked selection is a major driver of genetic diversity. Selection against deleterious mutations removes linked neutral diversity (background selection, BGS, Charlesworth et al. 1993), creating a positive correlation between recombination rates and genetic diversity. Purifying selection against recessive variants, however, can also lead to associative overdominance (AOD, Ohta 1971, Zhao & Charlesworth, 2016), due to an apparent heterozygote advantage at linked neutral loci that opposes the loss of neutral diversity by BGS. Zhao & Charlesworth (2016) identified the conditions when AOD should dominate over BGS in a single-locus model and suggested that the effect of AOD could become stronger if multiple linked deleterious variants co-segregate. We present a model describing how and under which conditions multi-locus dynamics can amplify the effects of AOD. We derive the conditions for a transition from BGS to AOD due to pseudo-overdominance (Ohta & Kimura 1970), i.e. a form of balancing selection that maintains complementary deleterious haplotypes that mask the effect of recessive deleterious mutations. Simulations confirm these findings and show that multi-locus AOD can increase diversity in low recombination regions much more strongly than previously appreciated. While BGS is known to drive genome-wide diversity in humans (Pouyet et al. 2018), the observation of a resurgence of genetic diversity in regions of very low recombination is indicative of AOD. We identify 21 such regions in the human genome showing clear signals of multi-locus AOD. Our results demonstrate that AOD may play an important role in the evolution of low recombination regions of many species.

scholarly journals Genomic signatures of rapid adaptive divergence in a tropical montane species

2021 ◽  
Vol 17 (7) ◽  
pp. 20210089
Author(s):  
Per G. P. Ericson ◽  
Martin Irestedt ◽  
Huishang She ◽  
Yanhua Qu
Keyword(s):  
Environmental Heterogeneity ◽  
Adaptive Divergence ◽  
Glacial Cycles ◽  
Genomic Signatures ◽  
Tropical Mountain ◽  
Population Genomic ◽  
Allopatric Divergence ◽  
Suitable Habitats ◽  
Genomic Regions ◽  
Two Populations

Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird ( Amblyornis papuensis ). Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.

scholarly journals Spontaneous whole-genome duplication restores fertility in interspecific hybrids

2019 ◽  
Author(s):  
Guillaume Charron ◽  
Souhir Marsit ◽  
Mathieu Hénault ◽  
Hélène Martin ◽  
Christian R. Landry
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Mitotic Cell ◽  
Whole Genome ◽  
Hybrid Speciation ◽  
Evolutionary Potential ◽  
Interspecies Hybrids ◽  
Ploidy Changes ◽  
Established Species ◽  
Fertility Recovery

AbstractInterspecies hybrids often show advantages over parents but suffer from reduced fertility, which can sometimes be overcome through sexual reproduction that sorts out incompatibilities. Sex is however inefficient due to the low viability or fertility of hybrid offspring and thus limits their evolutionary potential. Mitotic cell division could be an alternative to fertility recovery in facultative sexual species. To test this, we evolved under relaxed selection more than 600 diploid yeast hybrids between species that span 100,000 to 15 M years of divergence. We find that hybrids can recover fertility spontaneously and rapidly through whole-genome duplication. These events occurred in both hybrids between young and well-established species. Our results show that the instability of hybrid ploidy is a spontaneous path to fertility recovery.One Sentence SummaryPloidy changes potentiate hybrid speciation by leading to fertility recovery.

scholarly journals Population genetics of Paramecium mitochondrial genomes: recombination, mutational spectrum, and efficacy of selection

2018 ◽  
Author(s):  
Parul Johri ◽  
Georgi K. Marinov ◽  
Thomas G. Doak ◽  
Michael Lynch
Keyword(s):  
Gc Content ◽  
Purifying Selection ◽  
Mitochondrial Genomes ◽  
Unique Combination ◽  
Protein Coding ◽  
Unicellular Eukaryotes ◽  
Population Genomic ◽  
Outgroup Species ◽  
Multiple Species ◽  
Mutation Spectra

ABSTRACTThe evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate mitochondrial genomes exhibit a unique combination of characteristics, including a linear organization and the presence of multiple genes with no known function or detectable homologs in other eukaryotes. Here we study the variation of ciliate mitochondrial genomes both within and across thirteen highly diverged Paramecium species, including multiple species from the P. aurelia species complex, with four outgroup species: P. caudatum, P. multimicronucleatum, and two strains that may represent novel related species. We observe extraordinary conservation of gene order and protein-coding content in Paramecium mitochondria across species. In contrast, significant differences are observed in tRNA content and copy number, which is highly conserved in species belonging to the P. aurelia complex but variable among and even within the other Paramecium species. There is an increase in GC content from ~20% to ~40% on the branch leading to the P. aurelia complex. Patterns of polymorphism in population-genomic data and mutation-accumulation experiments suggest that the increase in GC content is primarily due to changes in the mutation spectra in the P. aurelia species. Finally, we find no evidence of recombination in Paramecium mitochondria and find that the mitochondrial genome appears to experience either similar or stronger efficacy of purifying selection than the nucleus.

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