Network science inspires novel tree shape statistics

Chindelevitch, Leonid; Hayati, Maryam; Poon, Art F. Y.; Colijn, Caroline

doi:10.1101/608646

Cited by 4 publications

(8 citation statements)

References 74 publications

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“…HIV and influenza virus trees The HIV trees were described and analyzed previously (Chindelevitch, 2019). Briefly, HIV-1 sequence data from three studies were used.…”

Section: Datamentioning

confidence: 99%

“…These datasets reflect a diverse set of spatial scales and epidemiological contexts. Phylogenetic reconstruction was described in (Chindelevitch, 2019); briefly, trees were reconstructed using RAxML (Stamatakis, 2014), which is a maximum likelihood method, under a general time-reversible (GTR) model of nucleotide substitution. We use a GTRCAT model for rate variation among sites.…”

Section: Datamentioning

confidence: 99%

“…As with influenza virus, it is to be hoped that these different epidemiological patterns are revealed in the shapes of reconstructed phylogenetic trees (Chindelevitch, 2019;. Figure 4.…”

Section: Applications To Datamentioning

confidence: 99%

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Polynomial Phylogenetic Analysis of Tree Shapes

Liu

Biller

Gould

et al. 2020

Preprint

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Phylogenetic trees are a central tool in evolutionary biology. They demonstrate evolutionary patterns among species, genes, and with modern sequencing technologies, patterns of ancestry among sets of individuals. Phylogenetic trees usually consist of tree shapes, branch lengths and partial labels. Comparing tree shapes is a main challenge in comparing phylogenetic trees as there are few tools to describe tree shapes in a quantitative, accurate, comprehensive and easy-to-interpret way. Current methods to compare tree shapes are often based on scalar indices reflecting tree imbalance, and on frequencies of small subtrees. Polynomials are important tools to describe discrete structures and have been used to study various objects including graphs and knots. There exist polynomials that describe rooted trees. In this paper, we present methods based on a polynomial that fully characterizes trees. These methods include tree metrics and machine learning tools. We use these methods to compare tree shapes randomly generated by simulations and tree shapes reconstructed from data. Moreover, we also show that the methods can be used to estimate parameters for tree shapes and select the best-fit model that generates the tree shapes.

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“…HIV and influenza virus trees The HIV trees were described and analyzed previously (Chindelevitch, 2019). Briefly, HIV-1 sequence data from three studies were used.…”

Section: Datamentioning

confidence: 99%

Section: Datamentioning

confidence: 99%

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Polynomial Phylogenetic Analysis of Tree Shapes

Liu

Biller

Gould

et al. 2020

Preprint

Self Cite

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“…There has been a growing interest in how network science can provide novel ways to characterize the shape of phylogenetic trees (Chindelevitch et al, 2019). We found that the shape of a phylogeny, and more specifically its stem-to-tip asymmetry increased-indicating more frequent terminal branching events (Lewitus and Morlon, 2016)-as the size of the refugia decreased compared to present, even more so if expansions occurred long ago.…”

Section: Phylogenetic Diversity Keeps Track Of (More) Ancient Habitat Changesmentioning

confidence: 82%

Imprints of Past Habitat Area Reduction on Extant Taxonomic, Functional, and Phylogenetic Composition

et al. 2021

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Past environmental changes have shaped the evolutionary and ecological diversity of extant organisms. Specifically, climatic fluctuations have made environmental conditions alternatively common or rare over time. Accordingly, most taxa have undergone restriction of their distribution to local refugia during habitat contraction, from which they could expand when suitable habitat became more common. Assessing how past restrictions in refugia have shaped species distributions and genetic diversity has motivated much research in evolutionary biology and biogeography. But there is still lack of clear synthesis on whether and how the taxonomic, functional and phylogenetic composition of extant multispecies assemblages retains the imprint of past restriction in refugia. We devised an original eco-evolutionary model to investigate the temporal dynamics of a regional species pool inhabiting a given habitat today, and which have experienced habitat reduction in the past. The model includes three components: (i) a demographic component driving stochastic changes in population sizes and extinctions due to habitat availability, (ii) a mutation and speciation component representing how divergent genotypes emerge and define new species over time, and (iii) a trait evolution component representing how trait values have changed across descendants over time. We used this model to simulate dynamics of multispecies assemblages that occupied a restricted refugia in the past and could expand their distribution subsequently. We characterized the past restriction in refugia in terms of two parameters representing the ending time of past refugia, and the extent of habitat restriction in the refugia. We characterized extant patterns of taxonomic, functional and phylogenetic diversity depending on these parameters. We found that extant relative abundances reflect the lasting influence of more recent refugia on demographic dynamics, while phylogenetic composition reflects the influence of more ancient habitat change. Extant functional diversity depends on the interplay between diversification dynamics and trait evolution, offering new options to jointly infer current trait adaptation and past trait evolution dynamics.

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“…first, fifth and sixth tree in Table 3. diameter (a) [15] maximal distance of two vertices diam(T ) := max i,j∈V (T )…”

Section: Normalizing Balance Indicesmentioning

confidence: 99%

Tree balance indices: a comprehensive survey

Fischer¹,

Herbst²,

Kersting³

et al. 2021

Preprint

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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 treebalance.wordpress.com containing fact sheets of the discussed indices. Moreover, we introduce the software package treebalance implemented in R that can be used to calculate all indices discussed.

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Network science inspires novel tree shape statistics

Cited by 4 publications

References 74 publications

Polynomial Phylogenetic Analysis of Tree Shapes

Polynomial Phylogenetic Analysis of Tree Shapes

Imprints of Past Habitat Area Reduction on Extant Taxonomic, Functional, and Phylogenetic Composition

Tree balance indices: a comprehensive survey

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