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Register a new userReview of haplotype complementarity under mutational pressure
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We discuss two different ways of chromosomes and genomes evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination processes are not effective enough to ensure an independent assortment of linked genes and larger clusters of genes could be inherited as the genetic units. There are whole clusters of genes which tend to complement in such conditions instead of single pairs of alleles like in the case of purifying selection. Computer simulations have shown that switching in-between complementation and purification strategies has a character of a phase transition. This is also responsible for specific distribution of recombination events observed along eukaryotic chromosomes - higher recombination rate is observed in subtelomeric regions than in central parts of chromosomes - for sympatric speciation and probably for non-monotonous relation between reproduction potential and genetic distance between parents.
Duality plays an important role in population genetics. It can relate results from forwards-in-time models of allele frequency evolution with those of backwards-in-time genealogical models; a well known example is the duality between the Wright-Fisher diffusion for genetic drift and its genealogical counterpart, the coalescent. There have been a number of articles extending this relationship to include other evolutionary processes such as mutation and selection, but little has been explored for models also incorporating crossover recombination. Here, we derive from first principles a new genealogical process which is dual to a Wright-Fisher diffusion model of drift, mutation, and recombination. Our approach is based on expressing a putative duality relationship between two models via their infinitesimal generators, and then seeking an appropriate test function to ensure the validity of the duality equation. This approach is quite general, and we use it to find dualities for several important variants, including both a discrete L-locus model of a gene and a continuous model in which mutation and recombination events are scattered along the gene according to continuous distributions. As an application of our results, we derive a series expansion for the transition function of the diffusion. Finally, we study in further detail the case in which mutation is absent. Then the dual process describes the dispersal of ancestral genetic material across the ancestors of a sample. The stationary distribution of this process is of particular interest; we show how duality relates this distribution to haplotype fixation probabilities. We develop an efficient method for computing such probabilities in multilocus models.
We study the dynamics of colonization of a territory by a stochastic population at low immigration pressure. We assume a sufficiently strong Allee effect that introduces, in deterministic theory, a large critical population size for colonization. At low immigration rates, the average pre-colonization population size is small thus invalidating the WKB approximation to the master equation. We circumvent this difficulty by deriving an exact zero-flux solution of the master equation and matching it with an approximate non-zero-flux solution of the pertinent Fokker-Planck equation in a small region around the critical population size. This procedure provides an accurate evaluation of the quasi-stationary probability distribution of population sizes in the pre-colonization state, and of the mean time to colonization, for a wide range of immigration rates. At sufficiently high immigration rates our results agree with WKB results obtained previously. At low immigration rates the results can be very different.
This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenskis long-term evolution experiment with Escherichia coli, where models aim at explaining the observed curve of the evolution of the mean fitness. The second part describes a model of a host-pathogen system where the population of pathogenes experiences balancing selection, migration, and mutation, as motivated by observations of the genetic diversity of HCMV (the human cytomegalovirus) across hosts.
Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing of parents. Applied to human and other vertebrate samples, our algorithm consistently outperforms existing single-sample assembly pipelines and generates assemblies of comparable quality to the best pedigree-based assemblies.
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