Recoverability of Ancestral Recombination Graph Topologies

Recombination is a powerful evolutionary process that shapes the genetic diversity observed in the populations of many species. Reconstructing genealogies in the presence of recombination from sequencing data is a very challenging problem, as this relies on mutations having occurred on the correct lineages in order to detect the recombination and resolve the placement of edges in the local trees. We investigate the probability of recovering the true topology of ancestral recombination graphs (ARGs)under the coalescent with recombination and gene conversion. We explore how sample size and mutation rate affect the inherent uncertainty in reconstructed ARGs; this sheds light on the theoretical limitations of ARG reconstruction methods. We illustrate our results using estimates of evolutionary rates for several biological organisms; in particular, we find that for parameter values that are realistic for SARS-CoV-2, the probability of reconstructing genealogies that are close to the truth is low

A characterisation of the genealogy of a birth-death process through time rescaling

The dynamics of a population exhibiting exponential growth can be modelled as a birth-death process, which naturally captures the stochastic variation in population size over time. In this article, we consider a supercritical birth-death process, started at a random time in the past, and conditioned to have n sampled individuals at the present. The genealogy of individuals sampled at the present time is then described by the reversed reconstructed process (RRP), which traces the ancestry of the sample backwards from the present. We show that a simple, analytic, time rescaling of the RRP provides a straightforward way to derive its inter-event times. The same rescaling characterises other distributions underlying this process, obtained elsewhere in the literature via more cumbersome calculations. We also consider the case of incomplete sampling of the population, in which each leaf of the genealogy is retained with an independent Bernoulli trial with probability \psi, and we show that corresponding results for Bernoulli-sampled RRPs can be derived using time rescaling, for any values of the underlying parameters. A central result is the derivation of a scaling limit as \psi approaches 0, corresponding to the underlying population growing to infinity, using the time rescaling formalism. We show that in this setting, after a linear time rescaling, the event times are the order statistics of n logistic random variables with mode \log(1/\psi); moreover, we show that the inter-event times are approximately exponentially distributed

Ongoing recombination in SARS-CoV-2 revealed through genealogical reconstruction

The evolutionary process of genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines. It can also significantly affect the results of phylogenetic analyses and the inference of evolutionary rates. The detection of recombination from samples of sequencing data is a very challenging problem and is further complicated for SARS-CoV-2 by its relatively slow accumulation of genetic diversity. The extent to which recombination is ongoing for SARS-CoV-2 is not yet resolved. To address this, we use a parsimony-based method to reconstruct possible genealogical histories for samples of SARS-CoV-2 sequences, which enables us to pinpoint specific recombination events that could have generated the data. We propose a statistical framework for disentangling the effects of recurrent mutation from recombination in the history of a sample, and hence provide a way of estimating the probability that ongoing recombination is present. We apply this to samples of sequencing data collected in England and South Africa and find evidence of ongoing recombination

Population genetics models for viral data with recombination

Utilising genetic sequencing data to infer the biological parameters that govern the evolution of a population is an important goal of population genetics. Common features of viral evolution mean that widely used modelling assumptions do not hold, such as that the population size is deterministic, that each site of the genome undergoes at most one mutation, or that recombination (individuals inheriting genetic material from two different parent genomes) is absent. In this thesis, models and methods are developed that relax these assumptions, and are thus particularly suited for the analysis of viral sequencing data. Birth-death process models naturally capture the stochastic variation and exponential growth in population size that is commonly seen, for instance, with intra-host viral populations. I investigate the properties of sample genealogies when the population evolves according to a birth-death process, and focus in particular on the setting of the population size growing to infinity. Through utilising a time rescaling formalism, distributions characterising the process are derived explicitly, and the results show that the genealogy has an interesting structure in this setting. The reconstruction of possible histories given a sample of genetic data in the presence of recombination is a challenging problem, and existing methods commonly assume the absence of recurrent mutation. I present KwARG, which implements a heuristic-based algorithm for finding plausible genealogical histories that are minimal or near-minimal in the number of posited recombination and recurrent mutation events. Through applying KwARG to reconstruct possible histories for samples of SARS-CoV-2 data, and combining the results with a principled statistical framework for recombination detection, I present evidence of ongoing recombination of SARS-CoV-2 within human hosts

The concept of kotodama as a fragment of Japanese linguocultural code

The purpose of the article is to study the concept of Kotodama, based on the Kotodama belief, and to analyze the role of this phenomenon in the Japanese linguoculture. In the course of the study, we reveal its origin, evolution and present status. The linguocultural and axiological approaches enable us to represent the main characteristics of Kotodama as an essential part of the Japanese language and culture

Prevalence rates of microsporidia in locusts and grasshoppers in South-Western Russia

Locusts and grasshoppers are dangerous polyphagous pests of agricultural crops. In the present paper, results of screening of Acridoidea populations in the South-Western Russia for microsporidia infections including locusts Locusta migratoria, Dociostaurus maroccanus, and Calliptamus italicus and grasshoppers Chorthippus loratus, Oedipoda caerulescens, and Acrida bicolor, are presented. Microsporidia prevalence rates were estimated using light microscopy of fresh smears. Out of 179 specimens of L. migratoria sampled between 2002 and 2019 in Krasnodar Territory, Astrakhan and Rostov Regions, none was infected with microsporidia. Similarly, 95 specimens of D. marrocanus from Krasnodar Territory (2017) and Dagestan Republic (2009) were also negative for microsporidia. Meanwhile, one positive case was detected for C. italicus corresponding to 0.5 % for the total amount of 192 exemplars collected from 2002 to 2019 in Krasnodar Territory, Astrakhan and Rostov Regions. As for grasshoppers, all Ch. loratus samplings in Krasnodar Territory in 2017-2019 were infected at the prevalence rates of 2.2-15 %, though no infection was found in 40 specimens in Crimea in 2019. In 56 individuals of O. caerulescens collected from Rostov Region and Krasnodar Territory, the microsporidia prevalence rate was 1.8 %. Among 96 specimens of A. bicolor, none was infected. In total, the microsporidia prevalence rates were higher in grasshoppers as compared to locusts, the difference being statistically significant at p<0.01

Susceptibility of three species of the genus

Microsporidia are obligate intracellular parasites that affect the population density of many insect pests. In particular, infection with Nosema pyrausta is one of the major mortality factors for the European corn borer Ostrinia nubilalis, the Asian corn borer Ostrinia furnacalis and the adzuki bean borer Ostrinia scapulalis. The purpose of the work is to compare the susceptibility to N. pyrausta and pathogenesis of three species of moths of the genus Ostrinia. Studies conducted over 2 years have shown that in all three species of host insects under laboratory conditions, both during oral infection and transovarian transmission of infection (in the daughter generations of experimentally infected insects), only diplokaryotic spores formed corresponding to the main morphotype of the genus Nosema. Mean lethal time increased with instar of larvae used for infection but didn’t differ between the three species. The rates of transovarial transmission of N. pyrausta were also similar. Thus, all the insect species examined may equally participate in the parasite persistence in nature and serve as model laboratory hosts for parasitological research and mass propagation of the microsporidium