scholarly journals The genetic architecture of recurrent segregation distortion in Arabidopsis thaliana

2017 ◽  
Author(s):  
Danelle K. Seymour ◽  
Eunyoung Chae ◽  
Burak I. Ariöz ◽  
Daniel Koenig ◽  
Detlef Weigel
Keyword(s):  
Arabidopsis Thaliana ◽  
Segregation Distortion ◽  
Evolutionary Biology ◽  
Genetic Material ◽  
Genomic Region ◽  
Epistatic Interactions ◽  
Reduced Representation ◽  
Central Tenet ◽  
Genetic Barriers ◽  
Gametic Selection

AbstractThe equal probability of transmission of alleles from either parent during sexual reproduction is a central tenet of genetics and evolutionary biology. Yet, there are many cases where this rule is violated. Such violations limit intraspecific gene flow and can facilitate the formation of genetic barriers, a first step in speciation. Biased transmission of alleles, or segregation distortion, can result from a number of biological processes including epistatic interactions between incompatible loci, gametic selection, and meiotic drive. Examples of these phenomena have been identified in many species, implying that they are universal, but comprehensive species-wide studies of segregation distortion are lacking. We have performed a species-wide screen for distorted allele frequencies in over 500 segregating populations of Arabidopsis thaliana using reduced-representation genome sequencing. Biased transmission of alleles was evident in up to a quarter of surveyed populations. Most populations exhibited distortion at only one genomic region, with some regions being repeatedly affected in multiple populations. Our results begin to elucidate the species-level architecture of biased transmission of genetic material in A. thaliana, and serve as a springboard for future studies into the basis of intraspecific genetic barriers.

scholarly journals On the Use of Blood Samples for Measuring DNA Methylation in Ecological Epigenetic Studies

2020 ◽  
Vol 60 (6) ◽  
pp. 1558-1566 ◽  
Author(s):  
Arild Husby
Keyword(s):  
Dna Methylation ◽  
Phenotypic Variation ◽  
Evolutionary Biology ◽  
Phenotypic Diversity ◽  
Genomic Region ◽  
Epigenetic Mechanism ◽  
Blood Samples ◽  
Reduced Representation ◽  
Bisulfite Treatment ◽  
Methylation Patterns

Synopsis There is increasing interest in understanding the potential for epigenetic factors to contribute to phenotypic diversity in evolutionary biology. One well studied epigenetic mechanism is DNA methylation, the addition of a methyl group to cytosines, which have the potential to alter gene expression depending on the genomic region in which it takes place. Obtaining information about DNA methylation at genome-wide scale has become straightforward with the use of bisulfite treatment in combination with reduced representation or whole-genome sequencing. While it is well recognized that methylation is tissue specific, a frequent limitation for many studies is that sampling-specific tissues may require sacrificing individuals, something which is generally undesirable and sometimes impossible. Instead, information about DNA methylation patterns in the blood is frequently used as a proxy tissue. This can obviously be problematic if methylation patterns in the blood do not reflect that in the relevant tissue. Understanding how, or if, DNA methylation in blood reflect DNA methylation patterns in other tissues is therefore of utmost importance if we are to make inferences about how observed differences in methylation or temporal changes in methylation can contribute to phenotypic variation. The aim of this review is to examine what we know about the potential for using blood samples in ecological epigenetic studies. I briefly outline some methods by which we can measure DNA methylation before I examine studies that have compared DNA methylation patterns across different tissues and, finally, examine how useful blood samples may be for ecological studies of DNA methylation. Ecological epigenetic studies are in their infancy, but it is paramount for the field to move forward to have detailed information about tissue and time dependence relationships in methylation to gain insights into if blood DNA methylation patterns can be a reliable bioindicator for changes in methylation that generate phenotypic variation in ecologically important traits.

scholarly journals Homozygosity at its Limit: Inbreeding Depression in Wild Arabidopsis arenosa Populations

2021 ◽  
Author(s):  
A. Cristina Barragan ◽  
Maximilian Collenberg ◽  
Rebecca Schwab ◽  
Merijn Kerstens ◽  
Ilja Bezrukov ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Inbreeding Depression ◽  
Genetic Material ◽  
Natural Populations ◽  
Outbreeding Depression ◽  
New Combinations ◽  
Epistatic Interactions ◽  
Hybrid Plants ◽  
Arabidopsis Arenosa

AbstractNew combinations of genetic material brought together through hybridization can lead to unfit offspring as a result of outbreeding or inbreeding depression. In selfing plants such as Arabidopsis thaliana, outbreeding depression is typically the result of pairwise deleterious epistatic interactions between two alleles that can geographically co-occur. What remains elusive is how often alleles resulting in genetic incompatibilities co-occur in natural populations of outcrossing plant species. To address this question, we screened over two thousand five hundred wild Arabidopsis arenosa hybrid plants in search for potential genetic mismatches. We show that although abnormal deleterious phenotypes are common, the transcriptional profiles of these abnormal A. arenosa plants differ substantially from those seen in incompatible A. thaliana hybrids. The abnormal hybrid phenotypes in A. arenosa had different underlying genetic architectures, yet a repeated theme was increased homozygosity, indicating that inbreeding rather than outbreeding depression gives rise to some of the deleterious phenotypes segregating in wild A. arenosa populations.

scholarly journals Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1269-1278 ◽  
Author(s):  
Bernhard Haubold ◽  
Jürgen Kroymann ◽  
Andreas Ratzka ◽  
Thomas Mitchell-Olds ◽  
Thomas Wiehe
Keyword(s):  
Genetic Diversity ◽  
Arabidopsis Thaliana ◽  
Linkage Disequilibrium ◽  
Gene Conversion ◽  
Genomic Sequence ◽  
Genomic Region ◽  
Resistance To Herbivory ◽  
Linkage Disequilibria ◽  
Coalescent Simulations ◽  
The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

scholarly journals Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Z. H. Forsman ◽  
R. Ritson-Williams ◽  
K.H. Tisthammer ◽  
I. S. S. Knapp ◽  
R. J. Toonen
Keyword(s):  
Genetic Structure ◽  
Evolutionary Biology ◽  
Species Complex ◽  
Coral Species ◽  
Genetic Relationships ◽  
Level Variation ◽  
Reduced Representation ◽  
The Pacific ◽  
Rapid Diversification ◽  
Candidate Loci

Abstract The ‘species’ is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The ‘Porites lobata species complex’ consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāneʻohe Bay Hawaiʻi during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.

Isolation and analysis of cDNA within a 300 kb Arabidopsis thaliana genomic region located around the 100 map unit of chromosome 1

Gene ◽  
1999 ◽  
Vol 239 (2) ◽  
pp. 309-316 ◽  
Author(s):  
Atsushi Kato ◽  
Masashi Suzuki ◽  
Ayuko Kuwahara ◽  
Hidekazu Ooe ◽  
Kumiko Higano-Inaba ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genomic Region ◽  
Chromosome 1

scholarly journals Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana

2008 ◽  
Vol 99 (4) ◽  
pp. 390-395 ◽  
Author(s):  
J. A. Schlueter ◽  
B. E. Scheffler ◽  
S. Jackson ◽  
R. C. Shoemaker
Keyword(s):  
Arabidopsis Thaliana ◽  
Glycine Max ◽  
Medicago Truncatula ◽  
Genomic Region ◽  
Duplicated Genes

scholarly journals The role of APETALA1 in petal number robustness

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Marie Monniaux ◽  
Bjorn Pieper ◽  
Sarah M McKim ◽  
Anne-Lise Routier-Kierzkowska ◽  
Daniel Kierzkowski ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Reproductive Success ◽  
Genetic Basis ◽  
Phenotypic Expression ◽  
Specific Difference ◽  
Closely Related Species ◽  
Epistatic Interactions ◽  
Species Specific

Invariant floral forms are important for reproductive success and robust to natural perturbations. Petal number, for example, is invariant in Arabidopsis thaliana flowers. However, petal number varies in the closely related species Cardamine hirsuta, and the genetic basis for this difference between species is unknown. Here we show that divergence in the pleiotropic floral regulator APETALA1 (AP1) can account for the species-specific difference in petal number robustness. This large effect of AP1 is explained by epistatic interactions: A. thaliana AP1 confers robustness by masking the phenotypic expression of quantitative trait loci controlling petal number in C. hirsuta. We show that C. hirsuta AP1 fails to complement this function of A. thaliana AP1, conferring variable petal number, and that upstream regulatory regions of AP1 contribute to this divergence. Moreover, variable petal number is maintained in C. hirsuta despite sufficient standing genetic variation in natural accessions to produce plants with four-petalled flowers.

Randomness in Evolution

2013 ◽  
Author(s):  
John Tyler Bonner
Keyword(s):  
Natural Selection ◽  
Evolutionary Biology ◽  
Biological Diversity ◽  
Large Mammals ◽  
Geological Time ◽  
Central Tenet ◽  
Morphological Differences

This book challenges a central tenet of evolutionary biology. The book makes the bold and provocative claim that some biological diversity may be explained by something other than natural selection. The book makes an argument for the underappreciated role that randomness—or chance—plays in evolution. Due to the tremendous and enduring influence of Darwin's natural selection, the importance of randomness has been to some extent overshadowed. The book shows how the effects of randomness differ for organisms of different sizes, and how the smaller an organism is, the more likely it is that morphological differences will be random and selection may not be involved to any degree. The book then traces the increase in size and complexity of organisms over geological time, and looks at the varying significance of randomness at different size levels, from microorganisms to large mammals. The book also discusses how sexual cycles vary depending on size and complexity, and how the trend away from randomness in higher forms has even been reversed in some social organisms.

scholarly journals Isolation of Ethyl Methanesulfonate-Induced Gametophytic Mutants in Arabidopsis thaliana by a Segregation Distortion Assay Using the Multimarker Chromosome 1

Genetics ◽  
1999 ◽  
Vol 151 (2) ◽  
pp. 849-863 ◽  
Author(s):  
Paul E Grini ◽  
Arp Schnittger ◽  
Heinz Schwarz ◽  
Inge Zimmermann ◽  
Birgit Schwab ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Life Cycle ◽  
Segregation Distortion ◽  
Marked Reduction ◽  
Marker Chromosome ◽  
Chromosome 1 ◽  
Phenotypic Analysis ◽  
Male And Female ◽  
Pollen Tube Elongation ◽  
And Function

Abstract The life cycle of plants comprises two alternating generations, the diploid sporophyte (spore-bearing plant) and the haploid gametophyte (gamete-bearing plant). In contrast to animals, the postmeiotic cells give rise to haploid organisms whose function is to produce the gametes and to mediate fertilization. Analysis of gametophyte development and function has been hampered by the difficulty of identifying haplo-phase-specific mutants in conventional mutagenesis screens. Here we use a genetic strategy that is based on segregation distortion of nearby visible markers to screen for EMS-induced gametophytic mutants in Arabidopsis thaliana. Using the multiple marker chromosome mm1 we have isolated seven lines that displayed an altered segregation of markers. Reciprocal backcrosses of these lines showed a marked reduction of the transmission of the male and/or female gametes. Phenotypic analysis revealed that different aspects of either gametophytic development or function were affected. Three male gametophytic lines showed specific arrests during pollen development. One male gametophytic line was specifically defective in pollen tube elongation. Three gametophytic lines showed variable defects in both male and female gametophytic development.

scholarly journals Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats

2017 ◽  
Vol 14 (127) ◽  
pp. 20160905 ◽  
Author(s):  
Pu Han ◽  
Michael W. Deem
Keyword(s):  
Phase Diagram ◽  
Evolutionary Biology ◽  
Bacterial Population ◽  
Genetic Material ◽  
Extinction Probability ◽  
Exposure Rate ◽  
Parameter Region ◽  
Predator Prey ◽  
Predator Prey Model ◽  
Two Phases

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator–prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR. When bacteria have a small rate of deleting spacers, a new parameter region in which bacteria and viruses can coexist arises, and it leads to a more complex coexistence patten for bacteria and viruses. For example, when the virus mutation rate is low, the virus extinction probability changes non-montonically with the bacterial exposure rate. The virus and bacteria coevolution not only alters the virus extinction probability, but also changes the bacterial population structure. Additionally, we show that recombination is a successful strategy for viruses to escape from CRISPR recognition when viruses have multiple proto-spacers, providing support for a recombination-mediated escape mechanism suggested experimentally. Finally, we suggest that the re-entrant phase diagram, in which phages can progress through three phases of extinction and two phases of abundance at low spacer deletion rates as a function of exposure rate to bacteria, is an experimentally testable phenomenon.

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