scholarly journals Effect of partial selfing and polygenic selection on establishment in a new habitat

2019 ◽  
Author(s):  
Himani Sachdeva
Keyword(s):  
Inbreeding Depression ◽  
Evolutionary Dynamics ◽  
High Rate ◽  
Source Population ◽  
Selfing Rate ◽  
Deleterious Alleles ◽  
Wide Range ◽  
Mate Limitation ◽  
Polygenic Selection

AbstractThis paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.

scholarly journals Eco-evolutionary dynamics of prior selfing rate promotes the coexistence without niche partitioning under reproductive interference

2020 ◽  
Author(s):  
Koki R. Katsuhara ◽  
Yuuya Tachiki ◽  
Ryosuke Iritani ◽  
Atushi Ushimaru
Keyword(s):  
Population Density ◽  
Plant Species ◽  
Inbreeding Depression ◽  
Evolutionary Dynamics ◽  
Niche Partitioning ◽  
Reproductive Interference ◽  
List Type ◽  
Selfing Rate ◽  
Evolutionary Rescue

AbstractWhen the two or more plants species share the same pollinators, pollinator-mediated reproductive interference make coexistence difficult. Recent studies suggested prior autonomous selfing mitigate reproductive interference, could enabling coexistence without pollination niche partitioning (pre-emptive selfing hypothesis). However, there are no studies to test whether evolution of prior selfing promote the coexistence, considering eco-evolutionary dynamics of population size, selfing rate and inbreeding depression.To examine conditions that the evolution of prior selfing promote coexistence under mutual reproductive interference especially in the point of view for pollinator availability and dynamics of inbreeding depression, we constructed individual-based model in which two plant species compete against each other in the form of mutual reproductive interference and can evolve prior autonomous selfing rate. We expected that purging of deleterious mutations could cause evolutionary rescue because inferior species could rescue population density through the evolution of prior selfing if the strength of inbreeding depression decreases with an increase of population’s selfing rate.Our simulation demonstrated that the evolution of prior selfing could promote the coexistence while reproductive interference caused competitive exclusion without evolution. We found that lower pollinator availability tended to prefer rapid evolutionary shift to higher prior selfing rate, it neutralizes the negative effect of reproductive interference, and population dynamics exhibit neutral random walk in both species. When the strength of inbreeding depression decreased with an increase in population’s selfing rate, moderate pollinator availability resulted in long-term coexistence in which relative-abundance-dependent selection on the prior selfing rate rescue population density of inferior species intermittently.Synthesis. We showed that the evolution of prior selfing could increase population growth rate of inferior species and consequently enable the long-term coexistence with evolutionary rescue. This is the new mechanisms explaining co-evolutionary coexistence of closely related plant species without niche partitioning and consistent with recent studies reported that closely related mixed-mating species are sympatrically growing even under the mutual reproductive interference.

scholarly journals Mutation load decreases with haplotype age in wild Soay sheep

2021 ◽  
Author(s):  
M.A. Stoffel ◽  
S.E. Johnston ◽  
J.G. Pilkington ◽  
J.M Pemberton
Keyword(s):  
Inbreeding Depression ◽  
Purifying Selection ◽  
Small Population ◽  
First Year ◽  
Mutation Load ◽  
Soay Sheep ◽  
Recessive Mutations ◽  
Deleterious Alleles ◽  
Lower Population

AbstractRuns of homozygosity (ROH) are pervasive in diploid genomes and expose the effects of deleterious recessive mutations, but how exactly these regions contribute to variation in fitness remains unclear. Here, we combined empirical analyses and simulations to explore the deleterious effects of ROH with varying genetic map lengths in wild Soay sheep. Using a long-term dataset of 4,592 individuals genotyped at 417K SNPs, we found that inbreeding depression increases with ROH length. A 1% genomic increase in long ROH (>12.5cM) reduced the odds of first-year survival by 12%, compared to only 7% for medium ROH (1.56-12.5cM), while short ROH (<1.56cM) had no effect on survival. We show by forward genetic simulations that this is predicted: compared with shorter ROH, long ROH will have higher densities of deleterious alleles, with larger average effects on fitness and lower population frequencies. Taken together, our results are consistent with the idea that the mutation load decreases in older haplotypes underlying shorter ROH, where purifying selection has had more time to purge deleterious mutations. Finally, our study demonstrates that strong inbreeding depression can persist despite ongoing purging in a historically small population.

scholarly journals Simulation of pedigree vs. fully-informative marker based relationships matrices in a loblolly pine breeding population

2021 ◽  
Author(s):  
Adam R Festa ◽  
Ross Whetten
Keyword(s):  
Inbreeding Depression ◽  
Loblolly Pine ◽  
Genetic Gain ◽  
Field Experiments ◽  
Breeding Value ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Genomic Relationship ◽  
Deleterious Alleles

Computer simulations of breeding strategies are an essential resource for tree breeders because they allow exploratory analyses into potential long-term impacts on genetic gain and inbreeding consequences without bearing the cost, time, or resource requirements of field experiments. Previous work has modeled the potential long-term implications on inbreeding and genetic gain using random mating and phenotypic selection. Reduction in sequencing costs has enabled the use of DNA marker-based relationship matrices in addition to or in place of pedigree-based allele sharing estimates; this has been shown to provide a significant increase in the accuracy of progeny breeding value prediction. A potential pitfall of genomic selection using genetic relationship matrices is increased coancestry among selections, leading to the accumulation of deleterious alleles and inbreeding depression. We used simulation to compare the relative genetic gain and risk of inbreeding depression within a breeding program similar to loblolly pine, utilizing pedigree-based or marker-based relationships over ten generations. We saw a faster rate of purging deleterious alleles when using a genomic relationship matrix based on markers that track identity-by-descent of segments of the genome. Additionally, we observed an increase in the rate of genetic gain when using a genomic relationship matrix instead of a pedigree-based relationship matrix. While the genetic variance of populations decreased more rapidly when using genomic-based relationship matrices as opposed to pedigree-based, there appeared to be no long-term consequences on the accumulation of deleterious alleles within the simulated breeding strategy.

Foundational Experiences and Recent Advances in Long-Term Deep-Ocean Borehole Observatories for Hydrologic, Geodetic, and Seismic Monitoring

2018 ◽  
Vol 52 (5) ◽  
pp. 74-86
Author(s):  
Earl Davis ◽  
Keir Becker ◽  
Masanori Kyo ◽  
Toshinori Kimura
Keyword(s):  
Subduction Zones ◽  
Deep Ocean ◽  
Data Access ◽  
High Rate ◽  
Time Data ◽  
Recent Advances ◽  
Early Results ◽  
Observatory Data ◽  
Wide Range

AbstractFor nearly three decades, various phases of the scientific Ocean Drilling Programs have deployed sealed-hole observatories in deep-ocean boreholes for long-term subseafloor monitoring to address a range of hydrologic and geodynamic objectives. We summarize the scientific motivation for these observatories and review some important early results from those installed in young oceanic crust and subduction zones. We also summarize the evolution of the borehole observatory designs and associated instrumentation, from simple single-interval installations with autonomous low-rate temperature and pressure monitoring to recent multiple-zone installations with sophisticated downhole instrument packages connected to seafloor cabled networks that provide power and high-rate, real-time data access. We emphasize recent advances, illustrated with example data drawn mainly from transects of borehole observatories offshore Japan and Cascadia. These examples illustrate the value of borehole observatory data in resolving a wide range of crustal geodynamic responses from long periods of gradual geodetic change and accumulation of stress to episodes of rapid deformation associated with both seafloor spreading and subduction processes.

scholarly journals Long-term exhaustion of the inbreeding load in Drosophila melanogaster

Heredity ◽  
2021 ◽  
Author(s):  
Noelia Pérez-Pereira ◽  
Ramón Pouso ◽  
Ana Rus ◽  
Ana Vilas ◽  
Eugenio López-Cortegano ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Evolutionary Biology ◽  
Gene Action ◽  
Large Population ◽  
Recessive Gene ◽  
Deleterious Alleles ◽  
Sib Mating ◽  
Large Populations ◽  
Great Relevance

AbstractInbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125–234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.

scholarly journals Ecological memory preserves phage resistance mechanisms in bacteria

2020 ◽  
Author(s):  
Antun Skanata ◽  
Edo Kussell
Keyword(s):  
Evolutionary Biology ◽  
Defense Mechanisms ◽  
Evolutionary Dynamics ◽  
Resistance Mechanisms ◽  
Term Survival ◽  
Linear Dynamical Systems ◽  
Ecological Memory ◽  
Wide Range ◽  
The Face

Defense mechanisms against pathogens are prevalent in nature, and their maintenance is critical for long-term survival of a species. Such mechanisms, which include CRISPR-mediated immunity in bacteria and the R genes in plants, carry substantial costs to organisms and can be rapidly lost when pathogens are eliminated. How a species preserves its molecular defenses despite their costs, in the face of variable pathogen levels, and across an ecology of localized patches remains a major unsolved problem in epidemiology and evolutionary biology. Using techniques of game theory and non-linear dynamical systems, we show that by maintaining a non-zero failure rate of immunity, hosts sustain sufficient levels of pathogen across an ecology to select against loss of the defense. This resistance switching strategy is evolutionarily stable, and provides a powerful evolutionary mechanism that maintains host-pathogen interactions and enables co-evolutionary dynamics in a wide range of systems.

scholarly journals The limits of long-term selection against Neandertal introgression

2018 ◽  
Author(s):  
Martin Petr ◽  
Svante Pääbo ◽  
Janet Kelso ◽  
Benjamin Vernot
Keyword(s):  
Negative Selection ◽  
Western Europe ◽  
Modern Human ◽  
Model Parameters ◽  
Modern Humans ◽  
High Coverage ◽  
The Past ◽  
Deleterious Alleles ◽  
Wide Range

AbstractSeveral studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans due to deleterious alleles that had accumulated in the Neandertals after they split from the modern human lineage. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45 thousand years. Here we show that this apparent decline is an artifact caused by gene flow between West Eurasians and Africans, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When applying a more robust statistic that takes advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Western Europe over the past 45 thousand years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters, and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular a depletion of Neandertal ancestry in conserved genomic regions that are likely to be of functional importance. Thus, we find that negative selection against Neandertal ancestry has not played as strong a role in recent human evolution as had previously been assumed.

scholarly journals Mating system of Datura inoxia: association between selfing rates and herkogamy within populations

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10698
Author(s):  
Vania Jiménez-Lobato ◽  
Juan Núñez-Farfán
Keyword(s):  
Mating System ◽  
Inbreeding Depression ◽  
Selfing Rate ◽  
Deleterious Alleles ◽  
Mating System Evolution ◽  
The Difference ◽  
Selfing Syndrome ◽  
Plant Mating System ◽  
Datura Inoxia ◽  
Plant Mating

Plant mating system determines, to a great extent, the demographic and genetic properties of populations, hence their potential for adaptive evolution. Variation in plant mating system has been documented between phylogenetically related species as well between populations of a species. A common evolutionary transition, from outcrossing to selfing, is likely to occur under environmental spatial variation in the service of pollinators. Here, we studied two phenotypically (in floral traits) and genetically (in neutral molecular markers) differentiated populations of the annual, insect-pollinated, plant Datura inoxia in Mexico, that differ in the service of pollinators (Mapimí and Cañada Moreno). First, we determined the populations’ parameters of phenotypic in herkogamy, outcrossing and selfing rates with microsatellite loci, and assessed between generation (adults and seedlings) inbreeding, and inbreeding depression. Second, we compared the relationships between parameters in each population. Results point strong differences between populations: plants in Mapimí have, on average, approach herkogamy, higher outcrossing rate (tm = 0.68), lower primary selfing rate (r = 0.35), and lower inbreeding at equilibrium (Fe = 0.24) and higher inbreeding depression (δ = 0.25), than the populations of Cañada. Outcrossing seems to be favored in Mapimí while selfing in Cañada. The relationship between r and Fe were negatively associated with herkogamy in Mapimí; here, progenies derived from plants with no herkogamy or reverse herkogamy had higher selfing rate and inbreeding coefficient than plants with approach herkogamy. The difference Fe–F is positively related to primary selfing rate (r) only in Cañada Moreno which suggests inbreeding depression in selfing individuals and then genetic purging. In conclusion, mating system evolution may occur differentially among maternal lineages within populations of Datura inoxia, in which approach herkogamy favors higher outcrossing rates and low levels of inbreeding and inbreeding depression, while no herkogamy or reverse herkogamy lead to the evolution of the “selfing syndrome” following the purge of deleterious alleles despite high inbreeding among individuals.

scholarly journals Multilocus models of inbreeding depression with synergistic selection and partial self-fertilization

1991 ◽  
Vol 57 (2) ◽  
pp. 177-194 ◽  
Author(s):  
B. Charlesworth ◽  
M. T. Morgan ◽  
D. Charlesworth
Keyword(s):  
Inbreeding Depression ◽  
Mutation Rate ◽  
Approximate Expression ◽  
Heterozygote Advantage ◽  
Selfing Rate ◽  
Deleterious Alleles ◽  
Plausible Model ◽  
Computer Calculations ◽  
Mean Fitness ◽  
The Mean

SummaryMean fitness and inbreeding depression values in multi-locus models of the control of fitness were studied, using both a model of mutation to deleterious alleles, and a model of heterozygote advantage. Synergistic fitness interactions between loci were assumed, to find out if this more biologically plausible model altered the conclusions we obtained previously using a model of multiplicative interactions. Systems of unlinked loci were assumed. We used deterministic computer calculations, and approximations based on normal or Poisson theory. These approximations gave good agreement with the exact results for some regions of the parameter space. In the mutational model, we found that the effect of synergism was to lower the number of mutant alleles per individual, and thus to increase the mean fitness, compared with the multiplicative case. Inbreeding depression, however, was increased. Similar effects on mean fitness and inbreeding depression were found for the case of heterozygote advantage. For that model, the results were qualitatively similar to those previously obtained assuming multiplicativity. With the mutational load model, however, the mean fitness sometimes decreased, and the inbreeding depression increased, at high selfing rates, after declining as the selfing rate increased from zero. We also studied the behaviour of modifier alleles that changed the selfing rate, introduced into equilibrium populations. In general, the results were similar to those with the multiplicative model, but in some cases an ESS selfing rate, with selfing slightly below one, existed. Finally, we derive an approximate expression for the inbreeding depression in completely selfing populations. This depends only on the mutation rate and the dominance coefficient and can therefore be used to obtain estimates of the mutation rate to mildly deleterious alleles for plant species.

Modern prevention and active longevity programs on the basis of disruptive domestic technologies: positive experience and prospects for application

2020 ◽  
pp. 66-73
Author(s):  
A. Simonova ◽  
S. Chudakov ◽  
R. Gorenkov ◽  
V. Egorov ◽  
A. Gostry ◽  
...  
Keyword(s):  
Personalized Medicine ◽  
Early Detection ◽  
Laboratory Diagnostics ◽  
Positive Experience ◽  
Practical Application ◽  
Wide Range ◽  
Integrated Program ◽  
Long Term Experience ◽  
Early Detection And Prevention

The article summarizes the long-term experience of practical application of domestic breakthrough technologies of preventive personalized medicine for laboratory diagnostics of a wide range of socially significant non-infectious diseases. Conceptual approaches to the formation of an integrated program for early detection and prevention of civilization diseases based on these technologies are given. A vision of the prospects for the development of this area in domestic and foreign medicine has been formed.

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