Anastasia Ignatieva's research while affiliated with University of Glasgow and other places
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Publications (11)
As a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). New developmen...
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 r...
Recent breakthroughs in the reconstruction of ancestral recombination graphs (ARGs) have meant that inference of genome-wide genealogies from large sequencing datasets is now possible. This development has also opened several new directions where research is urgently needed: improving our understanding of which aspects of genealogies are (and which...
Recombination is an ongoing and increasingly important feature of circulating lineages of SARS-CoV-2, challenging how we represent the evolutionary history of this virus and giving rise to new variants of potential public health concern by combining transmission and immune evasion properties of different lineages. Detection of new recombinant strai...
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 reco...
![Figure 15. Fixed θ = 100, varying breakpoint position z across [0, 0.5].](publication/355184699/figure/fig4/AS:1078831490310145@1634224879921/Fixed-th-100-varying-breakpoint-position-z-across-0-05_Q320.jpg)
A bstract
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 recombina...
Motivation
The reconstruction of possible histories given a sample of genetic data in the presence of recombination and recurrent mutation is a challenging problem, but can provide key insights into the evolution of a population. We present KwARG, which implements a parsimony-based greedy heuristic algorithm for finding plausible genealogical histo...
A bstract
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 detecti...
A bstract
The reconstruction of possible histories given a sample of genetic data in the presence of recombination and recurrent mutation is a challenging problem, but can provide key insights into the evolution of a population. We present KwARG, which implements a parsimony-based greedy heuristic algorithm for finding plausible genealogical histor...
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...
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. 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...
Citations
... Based on this observation, Kelleher et al. [29,30,44] introduce so-called tree sequences (Figure 1.a), which are collections of genealogical trees, each describing the evolutionary history of a range of adjacent sites along the genome. Conceptually, tree sequences are closely related to Ancestral Recombination Graphs [57]. In the genealogical trees stored in a tree sequence, tips represent biological samples, edges represent lines of descent, and mutations are meta-data stored at these edges ( Figure 1). ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/712393776697345-1546859320632_Q64/Gregor-Gorjanc.jpg)
... ARG inference will therefore tend to decline in accuracy when the ratio of mutations to recombination is low [45]. This tension between mutation and recombination imposes a theoretical limit on ARG recoverability from sequencing data [46]. ...
... ARG-Needle [60] constructs ARGs using the aforementioned threading approach, similar to ARGweaver, together with several heuristics and approximations to achieve scalability. The ability to infer genome-wide ARGs for large samples opens up new research directions [16,17] and has enabled a series of ARG-based applications in population and statistical genetics research [9,10,14,19,24,25,41,47,51,56]. ...
... The term ARG has been used to describe several different things in the literature (Wong et al., 2023). Related to our study, true ARGs are equivalent to the underlying real genealogical history of a sample set. ...
... n = 39 languages in Neureiter et al. [2022]). As viruses are known to be affected by recombination, we also expect future virus studies to use large network phylogenies Ignatieva et al. [2022], so that BP will become essential for network studies too. In this work, we describe approaches currently used for trait evolution on phylogenetic networks. ...
... It is a major goal of population genetics to infer rates of recombination along the genome and to disentangle its effects from other evolutionary forces such as mutation, selection, migration, and genetic drift. However, the effects of recombination can be difficult to detect; generally the signal of recombination is weak and a single recombination event may leave no discernible trace in a sample of genetic data (Hayman et al. 2022). Typically one observes a sample from the state of the population only at the present day, while the evolutionary history of the population, which can be much more informative for recombination, is a latent, unobserved variable. ...
... Griffiths and Marjoram, 1996) or explicit 166 information (e.g. Gusfield, 2014;Ignatieva et al., 2021) is required to distinguish the left and right 167 parents. We assume in Fig. 2 that d inherits genetic material to the left of x from e and to the right 168 of x from f. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/911462105112576-1594320908367_Q64/Rune-Lyngso.jpg)
... As such the question arises on the lack of recombination events reported for circulating SARS-CoV-2 viruses. There have been a limited number of publications reporting any such recombination events (31)(32)(33)(34). ...
... Although it is straightforward to simulate under this process (Hudson, 2002;Kelleher et al., 2016), inferring ARGs from population genetic variation data is a very challenging problem. Indeed, much algorithmic work has been done on reconstructing parsimonious histories with recombination (Hein, 1993;Gusfield et al., 2003;Song and Hein, 2003;Wang et al., 2001;Lyngsø et al., 2005;Gusfield, 2014;Ignatieva et al., 2020) and sampling ARGs under the coalescent with recombination (Griffiths and Marjoram, 1996;Fearnhead and Donnelly, 2001;Jenkins and Griffiths, 2011;Rasmussen et al., 2014). ...
... This earlier work takes a somewhat different approach where it is assumed that the moment at which a tree of unknown size and birth and death rates emerged is entirely unknown and is equally likely to have occurred at any time in the past. This amounts to assuming the age τ of any tree to follow an improper uniform distribution on [0, ∞) which is thus taken to be the prior (for a more recent application of this model assumption, see Ignatieva et al 2020). If the parameters n, λ and μ are known, application of Bayes' theorem gives rise to the posterior distribution for tree age density conditioned on n, λ, μ which, in the notation used by Gernhard (2008;theorem 3.2), is found to be ...
