scholarly journals Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum

Genetics ◽  
2018 ◽  
Vol 211 (3) ◽  
pp. 963-976 ◽  
Author(s):  
Pierre-Henri Clergeot ◽  
Nicolas O. Rode ◽  
Sylvain Glémin ◽  
Mikael Brandström Durling ◽  
Katarina Ihrmark ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Root Rot ◽  
Genetic Model ◽  
Diploid Species ◽  
Life Cycles ◽  
Deleterious Mutations ◽  
Mycelium Growth ◽  
Statistical Framework ◽  
Quantitative Genetic Model ◽  
Two Phases

Many eukaryote species, including taxa such as fungi or algae, have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance—a measure that accounts for these two effects—should be close to 0.5 in these species. It also predicts that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring, and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungus Heterobasidion parviporum—a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons, and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.

scholarly journals Estimating the fitness effect of deleterious mutations during the two phases of the life cycle: a new method applied to the root-rot fungusHeterobasidion parviporum

2018 ◽  
Author(s):  
Pierre-Henri Clergeot ◽  
Nicolas O. Rode ◽  
Sylvain Glémin ◽  
Mikael Brandström-Durling ◽  
Katarina Ihrmark ◽  
...  
Keyword(s):  
Growth Rate ◽  
Life Cycle ◽  
Genetic Distance ◽  
Root Rot ◽  
Genetic Model ◽  
Diploid Species ◽  
Life Cycles ◽  
Deleterious Mutations ◽  
Mycelium Growth ◽  
Two Phases

AbstractMany eukaryote species including taxa such as fungi or algae have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance, a measure that accounts for these two effects, should be close to 0.5 in these species. It also predicts that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungusHeterobasidion parviporum, a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.Article summary for Issue HighlightsMany eukaryote species including taxa such as fungi or algae spend a large portion of their life cycle as haploids and as diploids. Clergeot, Rodeet al.derive a statistical model to test whether deleterious mutations have stronger effects in homozygous diploids than in haploids, whether they are partially recessive in heterozygous diploids and whether diploids have higher fitness than haploids on average. As an illustration, they use their model to study growth rate and the ability to degrade wood in the root-rot fungusHeterobasidion parviporum. Their model should help gaining further insights into the evolution of haploid-diploid life cycles.

scholarly journals The Evolution of X-Linked Genomic Imprinting

Genetics ◽  
2001 ◽  
Vol 158 (4) ◽  
pp. 1801-1809 ◽  
Author(s):  
Yoh Iwasa ◽  
Andrew Pomiankowski
Keyword(s):  
Gene Expression ◽  
Gene Silencing ◽  
Experimental Evidence ◽  
Genomic Imprinting ◽  
Genetic Model ◽  
Deleterious Mutations ◽  
Genomic Conflict ◽  
Quantitative Genetic ◽  
Genetic Activity ◽  
Quantitative Genetic Model

Abstract We develop a quantitative genetic model to investigate the evolution of X-imprinting. The model compares two forces that select for X-imprinting: genomic conflict caused by polygamy and sex-specific selection. Genomic conflict can only explain small reductions in maternal X gene expression and cannot explain silencing of the maternal X. In contrast, sex-specific selection can cause extreme differences in gene expression, in either direction (lowered maternal or paternal gene expression), even to the point of gene silencing of either the maternal or paternal copy. These conclusions assume that the Y chromosome lacks genetic activity. The presence of an active Y homologue makes imprinting resemble the autosomal pattern, with active paternal alleles (X- and Y-linked) and silenced maternal alleles. This outcome is likely to be restricted as Y-linked alleles are subject to the accumulation of deleterious mutations. Experimental evidence concerning X-imprinting in mouse and human is interpreted in the light of these predictions and is shown to be far more easily explained by sex-specific selection.

scholarly journals A Reaction-Diffusion Model for Interference in Meiotic Crossing Over

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 365-372 ◽  
Author(s):  
Youhei Fujitani ◽  
Shintaro Mori ◽  
Ichizo Kobayashi
Keyword(s):  
Genetic Distance ◽  
Diffusion Model ◽  
Genetic Model ◽  
Initial Density ◽  
Reaction Diffusion ◽  
Crossover Point ◽  
Random Walker ◽  
Random Walkers ◽  
Reaction Diffusion Model ◽  
Two Parameters

Abstract One crossover point between a pair of homologous chromosomes in meiosis appears to interfere with occurrence of another in the neighborhood. It has been revealed that Drosophila and Neurospora, in spite of their large difference in the frequency of crossover points, show very similar plots of coincidence—a measure of the interference—against the genetic distance of the interval, defined as one-half the average number of crossover points within the interval. We here propose a simple reaction-diffusion model, where a “randomly walking” precursor becomes immobilized and matures into a crossover point. The interference is caused by pair-annihilation of the random walkers due to their collision and by annihilation of a random walker due to its collision with an immobilized point. This model has two parameters—the initial density of the random walkers and the rate of its processing into a crossover point. We show numerically that, as the former increases and/or the latter decreases, plotted curves of the coincidence vs. the genetic distance converge on a unique curve. Thus, our model explains the similarity between Drosophila and Neurospora without parameter values adjusted finely, although it is not a “genetic model” but is a “physical model,” specifying explicitly what happens physically.

Perennial grain crops: A synthesis of ecology and plant breeding

2005 ◽  
Vol 20 (1) ◽  
pp. 5-14 ◽  
Author(s):  
L.R. DeHaan ◽  
D.L. Van Tassel ◽  
T.S. Cox
Keyword(s):  
Plant Breeding ◽  
Environmental Changes ◽  
Genetic Model ◽  
Nutrient Loss ◽  
Trade Off ◽  
Grain Crops ◽  
Herbaceous Perennials ◽  
Quantitative Genetic ◽  
Quantitative Genetic Model ◽  
Perennial Grain

AbstractPerennial grain crops would address many agricultural problems, including soil erosion, nutrient loss and pesticide contamination. Doubts about the possibility of perennial grain crops rest upon two assumptions: (1) that the relationship between yield and longevity is a fixed function that cannot be influenced by selection, mutation or environmental changes; and (2) that yield and longevity trade off in a bivariate manner to the exclusion of all other traits. These assumptions are consistent with the phenotypic trade-off model, but recent research suggests that a quantitative genetic model is a more appropriate approach to trade-offs. In the quantitative genetic model, environmental and genetic changes can result in increases in two traits simultaneously even when a trade-off, or negative correlation, exists between the two traits. Empirical evidence that the trade-off between perenniality and reproductive allocation is not fixed comes from wild, herbaceous perennials that can produce more than 2000 kg seed ha−1 in the temperate zone, and herbaceous perennial crops that produce on average 8900 kg fruit ha−1 in the tropics. Ecological literature suggests that most perennials produce small amounts of seed relative to their vegetative growth not as a physiological absolute, but rather as a result of natural selection in a stable, competitive environment favoring longevity. By selecting strongly for seed yield in a population of perennial plants, the plant breeder can likely achieve that which is rare in nature—a high seed-yielding perennial plant. The same general methodologies that have allowed annual grain breeders to increase grain yield and push many combinations of negatively correlated traits to levels of expression not seen in nature are available to the perennial grain breeder. Perennial grain breeders are integrating ecological principles and traditional plant breeding methods in their efforts to develop perennial grain wheat (Triticum spp.), sorghum (Sorghum spp.), sunflower (Helianthus spp.), Illinois bundleflower (Desmanthus illinoensis) and rice (Oryza spp.).

scholarly journals Contrasting effects of intralocus sexual conflict on sexually antagonistic coevolution

2016 ◽  
Vol 113 (8) ◽  
pp. E978-E986 ◽  
Author(s):  
Tanya M. Pennell ◽  
Freek J. H. de Haas ◽  
Edward H. Morrow ◽  
G. Sander van Doorn
Keyword(s):  
Sexual Conflict ◽  
Genetic Model ◽  
Arms Races ◽  
Female Partners ◽  
Intralocus Sexual Conflict ◽  
Antagonistic Coevolution ◽  
Evolutionary Conflict ◽  
Quantitative Genetic Model ◽  
Female Specific ◽  
Evolutionary Consequences

Evolutionary conflict between the sexes can induce arms races in which males evolve traits that are detrimental to the fitness of their female partners, and vice versa. This interlocus sexual conflict (IRSC) has been proposed as a cause of perpetual intersexual antagonistic coevolution with wide-ranging evolutionary consequences. However, theory suggests that the scope for perpetual coevolution is limited, if traits involved in IRSC are subject to pleiotropic constraints. Here, we consider a biologically plausible form of pleiotropy that has hitherto been ignored in treatments of IRSC and arrive at drastically different conclusions. Our analysis is based on a quantitative genetic model of sexual conflict, in which genes controlling IRSC traits have side effects in the other sex, due to incompletely sex-limited gene expression. As a result, the genes are exposed to intralocus sexual conflict (IASC), a tug-of-war between opposing male- and female-specific selection pressures. We find that the interaction between the two forms of sexual conflict has contrasting effects on antagonistic coevolution: Pleiotropic constraints stabilize the dynamics of arms races if the mating traits are close to evolutionary equilibrium but can prevent populations from ever reaching such a state. Instead, the sexes are drawn into a continuous cycle of arms races, causing the buildup of IASC, alternated by phases of IASC resolution that trigger the next arms race. These results encourage an integrative perspective on the biology of sexual conflict and generally caution against relying exclusively on equilibrium stability analysis.

scholarly journals Rethinking competence in marine life cycles: ontogenetic changes in the settlement response of sand dollar larvae exposed to turbulence

2015 ◽  
Vol 2 (6) ◽  
pp. 150114 ◽  
Author(s):  
Jason Hodin ◽  
Matthew C. Ferner ◽  
Gabriel Ng ◽  
Christopher J. Lowe ◽  
Brian Gaylord
Keyword(s):  
Life Histories ◽  
Immature Stage ◽  
Life Cycles ◽  
Sand Dollar ◽  
Ontogenetic Changes ◽  
Marine Animals ◽  
Settlement And Metamorphosis ◽  
Two Phases ◽  
Pass Through ◽  
Dendraster Excentricus

Complex life cycles have evolved independently numerous times in marine animals as well as in disparate algae. Such life histories typically involve a dispersive immature stage followed by settlement and metamorphosis to an adult stage on the sea floor. One commonality among animals exhibiting transitions of this type is that their larvae pass through a ‘precompetent’ period in which they do not respond to localized settlement cues, before entering a ‘competent’ period, during which cues can induce settlement. Despite the widespread existence of these two phases, relatively little is known about how larvae transition between them. Moreover, recent studies have blurred the distinction between the phases by demonstrating that fluid turbulence can spark precocious activation of competence. Here, we further investigate this phenomenon by exploring how larval interactions with turbulence change across ontogeny, focusing on offspring of the sand dollar Dendraster excentricus (Eschscholtz). Our data indicate that larvae exhibit increased responsiveness to turbulence as they get older. We also demonstrate a likely cost to precocious competence: the resulting juveniles are smaller. Based upon these findings, we outline a new, testable conception of competence that has the potential to reshape our understanding of larval dispersal and connectivity among marine populations.

scholarly journals A General Quantitative Genetic Model for Haplotyping a Complex Trait in Humans

2007 ◽  
Vol 8 (5) ◽  
pp. 343-350 ◽  
Author(s):  
Song Wu ◽  
Jie Yang ◽  
Chenguang Wang ◽  
Rongling Wu
Keyword(s):  
Genetic Model ◽  
Complex Trait ◽  
Quantitative Genetic ◽  
Quantitative Genetic Model
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