scholarly journals Diversification or collapse of self-incompatibility haplotypes as outcomes of evolutionary rescue

2019 ◽  
Author(s):  
Alexander Harkness ◽  
Emma E. Goldberg ◽  
Yaniv Brandvain
Keyword(s):  
Gene Conversion ◽  
Balancing Selection ◽  
Markov Chain Model ◽  
Haplotype Diversity ◽  
Allelic Polymorphism ◽  
Chain Model ◽  
Self Incompatibility ◽  
Evolutionary Rescue ◽  
Large Populations ◽  
Incompatibility Locus

AbstractSelf-incompatibility systems in angiosperms are exemplars of extreme allelic polymorphism maintained by long-term balancing selection. Pollen that shares an allele with the pollen recipient at the self-incompatibility locus is rejected, and this rejection favors rare alleles as well as preventing self-fertilization. Advances in molecular genetics reveal that an ancient, deeply conserved, and well-studied incompatibility system functions through multiple tightly linked genes encoding separate pollen-expressed F-box proteins and pistil-expressed ribonucleases. We show that certain recombinant haplotypes at the incompatibility locus can drive collapse in the number of incompatibility types. We use a modified evolutionary rescue model to calculate the relative probabilities of increase and collapse in number of incompatibility types given the initial collection of incompatibility haplotypes and the population rate of gene conversion. We find that expansion in haplotype number is possible when population size or the rate of gene conversion is large, but large contractions are likely otherwise. By iterating a Markov chain model derived from these expansion and collapse probabilities, we find that a stable haplotype number distribution in the realistic range of 10–40 is possible under plausible parameters. However, small or moderate-sized populations should be susceptible to substantial additional loss of haplotypes beyond those lost by chance during bottlenecks. The same processes that can generate many incompatibility haplotypes in large populations may therefore be crushing haplotype diversity in smaller populations.

scholarly journals Diversification or collapse of self-incompatibility haplotypes as a rescue process

2020 ◽  
Author(s):  
Alexander Harkness ◽  
Emma E. Goldberg ◽  
Yaniv Brandvain
Keyword(s):  
Gene Conversion ◽  
Conversion Rate ◽  
Markov Chain Model ◽  
The Self ◽  
Allelic Polymorphism ◽  
Chain Model ◽  
Self Incompatibility ◽  
Recognition Mechanism ◽  
Self Recognition ◽  
Incompatibility Locus

AbstractIn angiosperm self-incompatibility systems, pollen with an allele matching the pollen recipient at the self-incompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequency-dependent selection favoring rare alleles. However, two challenges limit the spread of a new allele (a tightly linked haplotype in this case) under the widespread “collaborative non-self recognition” mechanism. First, there is no obvious selective benefit for pollen compatible with non-existent stylar incompatibilities, which themselves cannot spread if no pollen can fertilize them. However, a pistil-function mutation complementary to a previously neutral pollen mutation may spread if it restores self-incompatibility to a self-compatible intermediate. Second, we show that novel haplotypes can drive elimination of existing ones with fewer siring opportunities. We calculate relative probabilities of increase and collapse in haplotype number given the initial collection of incompatibility haplotypes and the population gene conversion rate. Expansion in haplotype number is possible when population gene conversion rate is large, but large contractions are likely otherwise. A Markov chain model derived from these expansion and collapse probabilities generates a stable haplotype number distribution in the realistic range of 10–40 under plausible parameters. However, smaller populations might lose many haplotypes beyond those lost by chance during bottlenecks.

An Efficient Markov Chain Model for the Simulation of Heterogeneous Soil Structure

2004 ◽  
Vol 68 (2) ◽  
pp. 346 ◽  
Author(s):  
Keijan Wu ◽  
Naoise Nunan ◽  
John W. Crawford ◽  
Iain M. Young ◽  
Karl Ritz
Keyword(s):  
Markov Chain ◽  
Soil Structure ◽  
Markov Chain Model ◽  
Chain Model ◽  
Heterogeneous Soil

Data Mining Technique Applied To DNA Sequencing

2015 ◽  
Vol 2 (7) ◽  
pp. 18
Author(s):  
R. Jamuna
Keyword(s):  
Data Mining ◽  
Dna Methylation ◽  
Markov Chain ◽  
Human Genome ◽  
Transition Probabilities ◽  
Markov Chain Model ◽  
Effective Means ◽  
Cpg Islands ◽  
Chain Model ◽  
The Given

CpG islands (CGIs) play a vital role in genome analysis as genomic markers.  Identification of the CpG pair has contributed not only to the prediction of promoters but also to the understanding of the epigenetic causes of cancer. In the human genome [1] wherever the dinucleotides CG occurs the C nucleotide (cytosine) undergoes chemical modifications. There is a relatively high probability of this modification that mutates C into a T. For biologically important reasons the mutation modification process is suppressed in short stretches of the genome, such as ‘start’ regions. In these regions [2] predominant CpG dinucleotides are found than elsewhere. Such regions are called CpG islands. DNA methylation is an effective means by which gene expression is silenced. In normal cells, DNA methylation functions to prevent the expression of imprinted and inactive X chromosome genes. In cancerous cells, DNA methylation inactivates tumor-suppressor genes, as well as DNA repair genes, can disrupt cell-cycle regulation. The most current methods for identifying CGIs suffered from various limitations and involved a lot of human interventions. This paper gives an easy searching technique with data mining of Markov Chain in genes. Markov chain model has been applied to study the probability of occurrence of C-G pair in the given   gene sequence. Maximum Likelihood estimators for the transition probabilities for each model and analgously for the  model has been developed and log odds ratio that is calculated estimates the presence or absence of CpG is lands in the given gene which brings in many  facts for the cancer detection in human genome.

scholarly journals Coevolution of theS-Locus GenesSRK,SLGandSP11/SCRinBrassica oleraceaandB. rapa

Genetics ◽  
2002 ◽  
Vol 162 (2) ◽  
pp. 931-940 ◽  
Author(s):  
Keiichi Sato ◽  
Takeshi Nishio ◽  
Ryo Kimura ◽  
Makoto Kusaba ◽  
Tohru Suzuki ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Gene Conversion ◽  
Phylogenetic Trees ◽  
Hypervariable Region ◽  
Recognition System ◽  
Self Incompatibility ◽  
Male And Female ◽  
Diversifying Selection ◽  
Tight Linkage ◽  
Nonsynonymous Site

AbstractBrassica self-incompatibility (SI) is controlled by SLG and SRK expressed in the stigma and by SP11/SCR expressed in the anther. We determined the sequences of the S domains of 36 SRK alleles, 13 SLG alleles, and 14 SP11 alleles from Brassica oleracea and B. rapa. We found three S haplotypes lacking SLG genes in B. rapa, confirming that SLG is not essential for the SI recognition system. Together with reported sequences, the nucleotide diversities per synonymous and nonsynonymous site (πS and πN) at the SRK, SLG, and SP11 loci within B. oleracea were computed. The ratios of πN:πS for SP11 and the hypervariable region of SRK were significantly >1, suggesting operation of diversifying selection to maintain the diversity of these regions. In the phylogenetic trees of 12 SP11 sequences and their linked SRK alleles, the tree topology was not significantly different between SP11 and SRK, suggesting a tight linkage of male and female SI determinants during the evolutionary course of these haplotypes. Genetic exchanges between SLG and SRK seem to be frequent; three such recent exchanges were detected. The evolution of S haplotypes and the effect of gene conversion on self-incompatibility are discussed.

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