arXiv subjects

Mareike Fischer

Publications and source records attributed to Mareike Fischer.

At least 19 recordsLinked to original sources

arXiv2026

Enumerating monophyletic characters in mathematical phylogenetics

Grouping species according to their phylogenetic relationships often results in different groups than grouping them according to their shared traits. Monophyletic groups play an important role in this regard, as they are groups of species sharing the same trait and being uniquely defined by a joint phylogenetic subtree. This immediately leads to the question of how to identify possible monophyletic groups in characters, which assign each present-day species a certain trait and which are typically used for phylogenetic tree reconstruction. In our manuscript, we provide a general formula to quantify how many different characters are monophyletic on any given tree and provide simple formulae for binary characters and for certain tree shapes. We also investigate relations between monophyly and the well-known phylogenetic tree reconstruction criterion maximum parsimony by providing a linear-time algorithm which determines the parsimony score together with the monophyly type of a character on a tree.

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arXiv2026

On Agreement Subtrees in Multiple Phylogenetic Trees

Snir and Yuster [Discrete Appl. Math. 347 (2026) 160--171] asked for the least number $h(k)$ such that $k$ unrooted binary phylogenetic trees on the same $h(k)$ leaves always share a common quartet. We give a new upper bound for the $k$-tree version of the Maximum Agreement Subtree problem, namely an upper bound for the number of leaves, on which $k$ unrooted binary phylogenetic trees always share a common induced binary subtree on $n$ leaves, which is a four-times iterated exponential function. For $h(k)$, this implies a four-times iterated exponential upper bound. We also set an exponential lower bound for $h(k)$.

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arXiv2026

Assessing 3D tree model quality and species classification using imbalance indices

We investigate the use of additional 3D and phylogenetic non-3D tree balance indices for analyzing and monitoring forests using an exemplary "virtual forest" dataset from the Wytham Woods, Oxford, UK. This study assesses 3D model quality, species classification performance, and the relevance of these indices. Our study shows that indices stemming from the study of ancestry trees of species can be successfully applied to 3D models of organic trees and, accompanied with recently introduced 3D imbalance indices, offer a complementary perspective on 3D tree models and improve the detection of deviations. Their computational efficiency combined with the simple and reproducible workflow presented in this manuscript form a computationally feasible quality control step in the 3D model construction. Species classification models reached an estimated accuracy of up to 81.8% and allowed to make confident species predictions for a large portion of the unlabeled trees in the dataset. While conventional tree metrics can already provide strong predictive performance, the addition of filtered 3D and non-3D statistics improved results consistently, particularly for minority species classes. Alongside this manuscript, we provide updated functionality in the R package treeDbalance to include the necessary functionalities and release the derived index datasets and species predictions.

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arXiv2026

A height-based metaconcept for rooted tree balance and its implications for the $B_1$ index

Tree balance has received considerable attention in recent years, both in phylogenetics and in other areas. Numerous (im)balance indices have been proposed to quantify the (im)balance of rooted trees. A recent comprehensive survey summarized this literature and showed that many existing indices are based on similar underlying principles. To unify these approaches, three general metaconcepts were introduced, providing a framework to classify, analyze, and extend imbalance indices. In this context, a metaconcept is a function $\Phi_f$ that depends on another function $f$ capturing some aspect of tree shape. In this manuscript, we extend this line of research by introducing a new metaconcept based on the heights of the pending subtrees of all inner vertices. We provide a thorough analysis of this metaconcept and use it to answer open questions concerning the well-known $B_1$ balance index. In particular, we characterize the tree shapes that maximize the $B_1$ index in two cases: (i) arbitrary rooted trees and (ii) binary rooted trees. For both cases, we also determine the corresponding maximum values of the index. Finally, while the $B_1$ index is induced by a so-called third-order metaconcept, we explicitly introduce three new (im)balance indices derived from the first- and second-order height metaconcepts, respectively, thereby demonstrating that pending subtree heights give rise to a variety of novel (im)balance indices.

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arXiv2025

Colorings of unrooted tree-based networks and related graphs

In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when reticulate evolutionary events happen, such as horizontal gene transfer or hybridization. But as such events are known to be relatively rare for most species, evolution is sometimes thought of as a process that can be represented by a tree with some additional edges, i.e., with a network that is still "somewhat tree-like". In this context, different versions of tree-based networks have played a major role in recent phylogenetic literature. Yet, surprisingly little is known about their combinatorial and graph-theoretic properties. In our manuscript, we answer a recently published question concerning the colorability of a specific class of tree-based networks. In particular, we will investigate an even more general class of graphs and show their 3-colorability. This nicely links recent phylogenetic concepts with classical graph theory. Moreover, the ideas we use to answer the colorability question are new and might potentially be generalizable to other coloring problems in graph theory.

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arXiv2025

Revealing the building blocks of tree balance: fundamental units of the Sackin and Colless Indices

(Im)balance indices can be used to quantify the (im)balance of trees by assigning numerical scores to them. An easy way to generate a new index is to construct a compound index, e.g., a linear combination of established indices. Two of the most prominent and widely used imbalance indices are the Sackin index and the Colless index. In this study, we show that these classic indices are themselves compound in nature: they can be decomposed into more elementary components that independently satisfy the defining properties of a tree (im)balance index. We further show that the difference Colless minus Sackin results in another imbalance index that is minimized (amongst others) by all Colless minimal trees. Conversely, the difference Sackin minus Colless forms a balance index. Finally, we compare the building blocks of which the Sackin and the Colless indices consist to these indices as well as to the stairs2 index, which is another index from the literature. Our results suggest that the elementary building blocks we identify are not only foundational to established indices but also valuable tools for analyzing disagreement among indices when comparing the balance of different trees. Along the way, we investigate the so-called echelon tree, which plays an important role for several (im)balance indices, and present the first non-recursive algorithm to construct it.

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arXiv2025

A strengthened bound on the number of states required to characterize maximum parsimony distance

In this article we prove that the distance $d_{\mathrm{MP}}(T_1,T_2) = k$ between two unrooted binary phylogenetic trees $T_1, T_2$ on the same set of taxa can be defined by a character that is convex on one of $T_1, T_2$ and which has at most $2k$ states. This significantly improves upon the previous bound of $7k-5$ states. We also show that for every $k \geq 1$ there exist two trees $T_1, T_2$ with $d_{\mathrm{MP}}(T_1,T_2) = k$ such that at least $k+1$ states are necessary in any character that achieves this distance and which is convex on one of $T_1, T_2$. We augment these lower and upper bounds with an empirical analysis which shows that in practice significantly fewer than $k+1$ states are usually required.

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arXiv2025

Metaconcepts of rooted tree balance

Measures of tree balance play an important role in many different research areas such as mathematical phylogenetics or theoretical computer science. Typically, tree balance is quantified by a single number which is assigned to the tree by a balance or imbalance index, of which several exist in the literature. Most of these indices are based on structural aspects of tree shape, such as clade sizes or leaf depths. For instance, indices like the Sackin index, total cophenetic index, and $\widehat{s}$-shape statistic all quantify tree balance through clade sizes, albeit with different definitions and properties. In this paper, we formalize the idea that many tree (im)balance indices are functions of similar underlying tree shape characteristics by introducing metaconcepts of tree balance. A metaconcept is a function $\Phi_f$ that depends on a function $f$ capturing some aspect of tree shape, such as balance values, clade sizes, or leaf depths. These metaconcepts encompass existing indices but also provide new means of measuring tree balance. The versatility and generality of metaconcepts allow for the systematic study of entire families of (im)balance indices, providing deeper insights that extend beyond index-by-index analysis.

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arXiv2025

The GFB Tree and Tree Imbalance Indices

Tree balance plays an important role in various research areas in phylogenetics and computer science. Typically, it is measured with the help of a balance index or imbalance index. There are more than 25 such indices available, recently surveyed in a book by Fischer et al. They are used to rank rooted binary trees on a scale from the most balanced to the least balanced. We show that a wide range of subtree-size based measures satisfying concavity and monotonicity conditions are minimized by the complete or greedy-from-the-bottom (GFB) tree and maximized by the caterpillar tree, yielding an infinitely large family of distinct new imbalance indices. Answering an open question from the literature, we show that one such established measure, the $\widehat{s}$-shape statistic, has the GFB tree as its unique minimizer. We also provide an alternative characterization of GFB trees, showing that they are equivalent to complete trees, which arise in different contexts. We give asymptotic bounds on the expected $\widehat{s}$-shape statistic under the uniform and Yule-Harding distributions of trees, and answer questions for the related $Q$-shape statistic as well.

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arXiv2024

Tree balance in phylogenetic models

Tree shape statistics, particularly measures of tree (im)balance, play an important role in the analysis of the shape of phylogenetic trees. With applications ranging from testing evolutionary models to studying the impact of fertility inheritance and selection, or tumor development and language evolution, the assessment of measures of tree balance is important. Currently, a multitude of at least 30 (im)balance indices can be found in the literature, alongside numerous other tree shape statistics. This diversity prompts essential questions: How can we assist researchers in choosing only a small number of indices to mitigate the challenges of multiple testing? Is there a preeminent balance index tailored to specific tasks? This research expands previous studies on the examination of index power, encompassing almost all established indices and a broader array of alternative models, such as a variety of trait-based models. Our investigation reveals distinct groups of balance indices better suited for different tree models, suggesting that decisions on balance index selection can be enhanced with prior knowledge. Furthermore, we present the \textsf{R} software package \textsf{poweRbal} which allows the inclusion of new indices and models, thus facilitating future research on the power of tree shape statistics.

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arXiv2024

On the correctness of Maximum Parsimony for data with few substitutions in the NNI neighborhood of phylogenetic trees

Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like maximum parsimony do not necessarily lead to unique trees and in some cases even fail to recognize the \enquote{correct} tree (i.e., the tree on which the data was generated). On the other hand, a recent study has shown that for an alignment containing precisely those binary characters (sites) which require up to two substitutions on a given tree, this tree will be the unique maximum parsimony tree. It is the aim of the present paper to generalize this recent result in the following sense: We show that for a tree $T$ with $n$ leaves, as long as $k<\frac{n}{8}+\frac{11}{9}-\frac{1}{18}\sqrt{9\cdot \left(\frac{n}{4}\right)^2+16}$ (or, equivalently, $n>9 k-11+\sqrt{9k^2-22 k+17} $, which in particular holds for all $n\geq 12k$), the maximum parsimony tree for the alignment containing all binary characters which require (up to or precisely) $k$ substitutions on $T$ will be unique in the NNI neighborhood of $T$ and it will coincide with $T$, too. In other words, within the NNI neighborhood of $T$, $T$ is the unique most parsimonious tree for the said alignment. This partially answers a recently published conjecture affirmatively. Additionally, we show that for $n\geq 8$ and for $k$ being in the order of $\frac{n}{2}$, there is always a pair of phylogenetic trees $T$ and $T'$ which are NNI neighbors, but for which the alignment of characters requiring precisely $k$ substitutions each on $T$ in total requires fewer substitutions on $T'$.

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arXiv2024

A complete characterization of pairs of binary phylogenetic trees with identical $A_k$-alignments

Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP). It is believed that the latter is able to reconstruct the \enquote{true} tree, i.e., the tree that generated the data, whenever the number of substitutions required to explain the data with that tree is relatively small compared to the size of the tree (measured in the number $n$ of leaves of the tree, which represent the species under investigation). However, reconstructing the correct tree from any alignment first and foremost requires the given alignment to perform differently on the \enquote{correct} tree than on others. A special type of alignments, namely so-called $A_k$-alignments, has gained considerable interest in recent literature. These alignments consist of all binary characters (\enquote{sites}) which require precisely $k$ substitutions on a given tree. It has been found that whenever $k$ is small enough (in comparison to $n$), $A_k$-alignments uniquely characterize the trees that generated them. However, recent literature has left a significant gap between $n\leq 2k+2$ -- namely the cases in which no such characterization is possible -- and $n\geq 4k$ -- namely the cases in which this characterization works. It is the main aim of the present manuscript to close this gap, i.e., to present a full characterization of all pairs of trees that share the same $A_k$-alignment. In particular, we show that indeed every binary phylogenetic tree with $n$ leaves is uniquely defined by its $A_k$-alignments if $n\geq 2k+3$. By closing said gap, we also ensure that our result is optimal.

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arXiv2024

The weighted total cophenetic index: A novel balance index for phylogenetic networks

Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has provided a lot of progress concerning the reconstruction of such networks from data as well as insight into their graph theoretical properties. However, methods and tools to quantify structural properties of networks or differences between them are still very limited. For example, for phylogenetic trees, it is common to use balance indices to draw conclusions concerning the underlying evolutionary model, and more than twenty such indices have been proposed and are used for different purposes. One of the most frequently used balance index for trees is the so-called total cophenetic index, which has several mathematically and biologically desirable properties. For networks, on the other hand, balance indices are to-date still scarce. In this contribution, we introduce the \textit{weighted} total cophenetic index as a generalization of the total cophenetic index for trees to make it applicable to general phylogenetic networks. As we shall see, this index can be determined efficiently and behaves in a mathematical sound way, i.e., it satisfies so-called locality and recursiveness conditions. In addition, we analyze its extremal properties and, in particular, we investigate its maxima and minima as well as the structure of networks that achieve these values within the space of so-called level-$1$ networks. We finally briefly compare this novel index to the two other network balance indices available so-far.

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arXiv2023

Measuring 3D tree imbalance of plant models using graph-theoretical approaches

Imbalance in the 3D structure of plants can be an important indicator of insufficient light or nutrient supply, as well as excessive wind, (formerly present) physical barriers, neighbor or storm damage. It can also be a simple means to detect certain illnesses, since some diseases like the apple proliferation disease, an infection with the barley yellow dwarf virus or plant canker can cause abnormal growth, like \enquote{witches' brooms} or burls, resulting in a deviating 3D plant architecture. However, quantifying imbalance of plant growth is not an easy task, and it requires a mathematically sound 3D model of plants to which imbalance indices can be applied. Current models of plants are often based on stacked cylinders or voxel matrices and do not allow for measuring the degree of 3D imbalance in the branching structure of the whole plant. On the other hand, various imbalance indices are readily available for so-called graph-theoretical trees and are frequently used in areas like phylogenetics and computer science. While only some basic ideas of these indices can be transferred to the 3D setting, graph-theoretical trees are a logical foundation for 3D plant models that allow for elegant and natural imbalance measures. In this manuscript, our aim is thus threefold: We first present a new graph-theoretical 3D model of plants and discuss desirable properties of imbalance measures in the 3D setting. We then introduce and analyze eight different 3D imbalance indices and their properties. Thirdly, we illustrate all our findings using a data set of 63 bush beans. Moreover, we implemented all our indices in the publicly available \textsf{R}-software package \textsf{treeDbalance} accompanying this manuscript.

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arXiv2023

Tree balance indices: a comprehensive survey

Tree balance plays an important role in phylogenetics and other research areas, which is why several indices to measure tree balance have been introduced over the years. Nevertheless, a formal definition of what a balance index actually is and what makes it a useful measure of balance (or, in other cases, imbalance), has so far not been introduced in the literature. While the established indices all summarize the (im)balance of a tree in a single number, they vary in their definitions and underlying principles. It is the aim of the present manuscript to introduce formal definitions of balance and imbalance indices that classify desirable properties of such indices and to analyze and categorize established indices accordingly. In this regard, we review 19 established (im)balance indices from the literature, summarize their general, statistical and combinatorial properties (where known), prove numerous additional results and indicate directions for future research by making explicit open questions and gaps in the literature. We also prove that a few tree shape statistics that have been used to measure tree balance in the literature do not fulfill our definition of an (im)balance index, which might indicate that their properties are not as useful for practical purposes. Moreover, we show that five additional tree shape statistics from other contexts actually are tree (im)balance indices according to our definition. The manuscript is accompanied by the website \url{treebalance.wordpress.com} containing fact sheets of the discussed indices. Moreover, we introduce the software package \verb|treebalance| implemented in $\mathsf{R}$ that can be used to calculate all indices discussed.

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arXiv2023

Defining binary phylogenetic trees using parsimony: new bounds

Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has been assumed to work well for data with only few state changes. Recently, some progress has been made to formally prove this assertion. For instance, it has been shown that each binary phylogenetic tree $T$ with $n \geq 20k$ leaves is uniquely defined by the set $A_k(T)$, which consists of all characters with parsimony score $k$ on $T$. In the present manuscript, we show that the statement indeed holds for all $n \geq 4k$, thus drastically lowering the lower bound for $n$ from $20k$ to $4k$. However, it has been known that for $n \leq 2k$ and $k \geq 3$, it is not generally true that $A_k(T)$ defines $T$. We improve this result by showing that the latter statement can be extended from $n \leq 2k$ to $n \leq 2k+2$. So we drastically reduce the gap of values of $n$ for which it is unknown if trees $T$ on $n$ taxa are defined by $A_k(T)$ from the previous interval of $[2k+1,20k-1]$ to the interval $[2k+3,4k-1]$. Moreover, we close this gap completely for the nearest neighbor interchange (NNI) neighborhood of $T$ in the following sense: We show that as long as $n\geq 2k+3$, no tree that is one NNI move away from $T$ (and thus very similar to $T$) shares the same $A_k$-alignment.

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arXiv2022

Defining binary phylogenetic trees using parsimony

Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple optimization criterion for such reconstructions is maximum parsimony. It is generally assumed that this criterion works well for data in which state changes are rare. In the present manuscript, we prove that each phylogenetic tree $T$ with $n\geq 20 k$ leaves is uniquely defined by the set $A_k(T)$, which consists of all characters with parsimony score $k$ on $T$. This can be considered as a promising first step towards showing that maximum parsimony as a tree reconstruction criterion is justified when the number of changes in the data is relatively small.

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arXiv2022

Effects of discordance between species and gene trees on phylogenetic diversity conservation

Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into account the unique and shared evolutionary history of each species as indicated by its placement in an underlying phylogenetic tree. Traditionally, phylogenetic trees were inferred from single genes and the resulting gene trees were assumed to be a valid estimate for the species tree, i.e., the "true" evolutionary history of the species under consideration. However, nowadays it is common to sequence whole genomes of hundreds or thousands of genes, and it is often the case that conflicting genealogical histories exist in different genes throughout the genome, resulting in discordance between individual gene trees and the species tree. Here, we analyze the effects of gene and species tree discordance on prioritization decisions based on the FP index. In particular, we consider the ranking order of taxa induced by (i) the FP index on a species tree, and (ii) the expected FP index across all gene tree histories associated with the species tree. On one hand, we show that for particular tree shapes, the two rankings always coincide. On the other hand, we show that for all leaf numbers greater than or equal to five, there exist species trees for which the two rankings differ. Finally, we illustrate the variability in the rankings obtained from the FP index across different gene tree and species tree estimates for an empirical multilocus mammal data set.

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