Polyploidization, whereby an organism inherits multiple copies of the genome of their parents, is an important evolutionary event that has been observed in plants and animals. One way to study such ...events is in terms of the ploidy number of the species that make up a dataset of interest. It is therefore natural to ask: How much information about the evolutionary past of the set of species that form a dataset can be gleaned from the ploidy numbers of the species? To help answer this question, we introduce and study the novel concept of a ploidy profile which allows us to formalize it in terms of a multiplicity vector indexed by the species the dataset is comprised of. Using the framework of a phylogenetic network, we present a closed formula for computing the
hybrid number
(i.e. the minimal number of polyploidization events required to explain a ploidy profile) of a large class of ploidy profiles. This formula relies on the construction of a certain phylogenetic network from the simplification sequence of a ploidy profile and the hybrid number of the ploidy profile with which this construction is initialized. Both of them can be computed easily in case the ploidy numbers that make up the ploidy profile are not too large. To help illustrate the applicability of our approach, we apply it to a simplified version of a publicly available Viola dataset.
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in ...evolutionary histories. An
unrooted
phylogenetic network on a non-empty, finite set
X
of taxa, or
network
, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is
X
. It is called a
phylogenetic tree
if the underlying graph is a tree. In this paper we consider properties of
tree-based networks
, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that ...phylogenetic networks offer themselves as a framework to reconstruct the evolutionary past of species affected by it. The main strategy for doing this is to first construct a so-called multiple-labelled tree and to then somehow derive such a network from it. The following question therefore arises: How much can be said about that past if such a tree is not readily available? By viewing a polyploid dataset as a certain vector which we call a ploidy (level) profile, we show that among other results, there always exists a phylogenetic network in the form of a beaded phylogenetic tree with additional arcs that realizes a given ploidy profile. Intriguingly, the two end vertices of almost all of these additional arcs can be interpreted as having co-existed in time thereby adding biological realism to our network, a feature that is, in general, not enjoyed by phylogenetic networks. In addition, we show that our network may be viewed as a generator of ploidy profile space, a novel concept similar to phylogenetic tree space that we introduce to be able to compare phylogenetic networks that realize one and the same ploidy profile. We illustrate our findings in terms of a publicly available Viola dataset.
Background and Aims
Anti‐mitochondrial antibodies (AMA) are closely linked to primary biliary cholangitis (PBC). The prevalence of AMA in the general population is low, and AMA positivity may precede ...PBC. We aimed to determine the natural history of subjects with positive AMA.
Methods
In total, 302 patients were tested AMA‐positive over a ten‐year period. Of these, immunoblotting confirmed specific AMA in 184 (29 male, 155 female, age 59.6 ± 14.1 years). These subjects were invited to our liver outpatient clinic for clinical and biochemical re‐evaluation. Detailed clinical history data were additionally collected from the hospital computer system and by telephone. The subsequent course with regard to mortality, liver‐related morbidity, extrahepatic co‐morbidities and effectiveness of PBC treatment was determined in 150 subjects (81.5%).
Results
After 5.8 ± 5.6 years of follow‐up (FU), of 184 AMA‐positive subjects, 28 subjects (15.2%; liver‐related mortality n = 5) were deceased, and 122 subjects (66.3%) completed FU while 34 subjects (18.5%) were not available for FU. The 122 patients who completed FU were 63 patients with established PBC, six de novo cases of PBC (10.2% of 59 initially at risk), 42 (34.4%) subjects were still AMA‐positive without PBC, and 11 (9.0%) subjects were AMA‐negative at FU.
Conclusions
Anti‐mitochondrial antibodies‐positive patients without PBC at baseline infrequently developed PBC over six years of FU. AMA positivity represented a transient serological autoimmune phenomenon in a significant proportion of subjects.
This Letter reports a measurement of the flux and energy spectrum of electron antineutrinos from six 2.9 GWth nuclear reactors with six detectors deployed in two near (effective baselines 512 and 561 ...m) and one far (1579 m) underground experimental halls in the Daya Bay experiment. Using 217 days of data, 296 721 and 41 589 inverse β decay (IBD) candidates were detected in the near and far halls, respectively. The measured IBD yield is (1.55±0.04) ×10(-18) cm(2) GW(-1) day(-1) or (5.92±0.14) ×10(-43) cm(2) fission(-1). This flux measurement is consistent with previous short-baseline reactor antineutrino experiments and is 0.946±0.022 (0.991±0.023) relative to the flux predicted with the Huber-Mueller (ILL-Vogel) fissile antineutrino model. The measured IBD positron energy spectrum deviates from both spectral predictions by more than 2σ over the full energy range with a local significance of up to ∼4σ between 4-6 MeV. A reactor antineutrino spectrum of IBD reactions is extracted from the measured positron energy spectrum for model-independent predictions.
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial ...objects used to construct them are triplet systems and cluster systems, the motivation being that any network
N
induces a triplet system
R
(
N
)
and a softwired cluster system
S
(
N
)
. Since in real-world studies it cannot be guaranteed that all triplets/softwired clusters induced by a network are available, it is of particular interest to understand whether subsets of
R
(
N
)
or
S
(
N
)
allow one to uniquely reconstruct the underlying network
N
. Here we show that even within the highly restricted yet biologically interesting space of level-1 phylogenetic networks it is not always possible to uniquely reconstruct a level-1 network
N
, even when all triplets in
R
(
N
)
or all clusters in
S
(
N
)
are available. On the positive side, we introduce a reasonably large subclass of level-1 networks the members of which are uniquely determined by their induced triplet/softwired cluster systems. Along the way, we also establish various enumerative results, both positive and negative, including results which show that certain special subclasses of level-1 networks
N
can be uniquely reconstructed from proper subsets of
R
(
N
)
and
S
(
N
)
. We anticipate these results to be of use in the design of algorithms for phylogenetic network inference.
Introgression is an evolutionary process in which genes or other types of genetic material are introduced into a genome. It is an important evolutionary process that can, for example, play a ...fundamental role in speciation. Recently the concept of an overlaid species forest (OSF) was introduced as a discrete way to model introgression. Basically, an OSF consists of a gene history in the form of a phylogenetic tree, a collection of lineage trees or forest for some species of interest, and a map that overlays the gene tree onto the forest. In this paper we shall study mathematical properties of OSFs and their relationship with other structures in phylogenetics, such as lateral gene transfer models, subtree prune and regraft operations, and phylogenetic networks. In particular, we show that a certain algorithm called OSF-Builder for constructing an OSF is guaranteed to produce a special type of OSF with a minimum number of introgressions, as well as providing some characterizations for networks that can arise from OSFs. We also give bounds on how much an OSF can change when the underlying gene tree or forest is perturbed. We expect that these results will be useful in developing new algorithms for deriving introgression histories, a rapidly growing area of interest in phylogenomics.
•Overlaid species forests (OSFs) model genes jumping between species lineages.•OSF-Builder algorithm produces a minimal OSF with a special structure.•We characterize phylogenetic networks that can arise from OSFs.•We quantify and bound OSF change when perturbing the underlying graph structure.
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim ...to construct phylogenetic networks from biological data using
triplets
, i.e. binary phylogenetic trees on 3-element subsets of a given set of species. However, a fundamental problem with this approach is that the triplets displayed by a phylogenetic network do not necessarily uniquely determine or
encode
the network. Here we propose an alternative approach to encoding and constructing phylogenetic networks, which uses phylogenetic networks on 3-element subsets of a set, or
trinets
, rather than triplets. More specifically, we show that for a special, well-studied type of phylogenetic network called a 1-nested network, the trinets displayed by a 1-nested network always encode the network. We also present an efficient algorithm for deciding whether a
dense
set of trinets (i.e. one that contains a trinet on every 3-element subset of a set) can be displayed by a 1-nested network or not and, if so, constructs that network. In addition, we discuss some potential new directions that this new approach opens up for constructing and comparing phylogenetic networks.
Forest-Based Networks Huber, K. T.; Moulton, V.; Scholz, G. E.
Bulletin of mathematical biology,
2022/10, Volume:
84, Issue:
10
Journal Article
Peer reviewed
Open access
In evolutionary studies, it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between ...the species or their ancestors has occurred in the past, a tree may not provide a complete picture of their history. In such cases,
tree-based phylogenetic networks
can provide a useful, more refined representation of the species’ evolution. Such a network is essentially a phylogenetic tree with some arcs added between the tree’s edges so as to represent reticulate events such as gene transfer, hybridization and recombination. Even so, this model does not permit the direct representation of evolutionary scenarios where reticulate events have taken place between different subfamilies or lineages of species. To represent such scenarios, in this paper we introduce the notion of a
forest-based network
, that is, a collection of leaf-disjoint phylogenetic trees on a set of species with arcs added between the edges of distinct trees within the collection. Forest-based networks include the recently introduced class of
overlaid species forests
which can be used to model
introgression
. As we shall see, even though the definition of forest-based networks is closely related to that of tree-based networks, they lead to new mathematical theory which complements that of tree-based networks. As well as studying the relationship of forest-based networks with other classes of phylogenetic networks, such as tree-child networks and universal tree-based networks, we present some characterizations of some special classes of forest-based networks. We expect that our results will be useful for developing new models and algorithms to understand reticulate evolution, such as introgression and gene transfer between species.
In-source resonant ionization laser spectroscopy of the even-A polonium isotopes (192-210,216,218)Po has been performed using the 6p(3)7s (5)S(2) to 6p(3)7p (5)P(2) (λ=843.38 nm) transition in the ...polonium atom (Po-I) at the CERN ISOLDE facility. The comparison of the measured isotope shifts in (200-210)Po with a previous data set allows us to test for the first time recent large-scale atomic calculations that are essential to extract the changes in the mean-square charge radius of the atomic nucleus. When going to lighter masses, a surprisingly large and early departure from sphericity is observed, which is only partly reproduced by beyond mean field calculations.
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