A Metric on Phylogenetic Tree Shapes

Colijn, Caroline; Plazzotta, Giacomo

doi:10.1093/sysbio/syx046

Cited by 54 publications

(64 citation statements)

References 58 publications

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“…Bursts in transmissibility are emblematic of increases in relative viral fitness and are reflected in 5 imbalances in the phylogeny, which can be estimated at each internal node (Figure S3) (25)(26)(27).…”

Section: Indicators Of Viral Evolution Have Been Shown To Be Robust Pmentioning

confidence: 99%

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

Dearlove

Lewitus

Bai

et al. 2020

Preprint

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The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Here we analyzed SARS-CoV-2 sequence diversity across 5,700 sequences sampled since December 2019. The Spike protein, which is the target immunogen of most vaccine 5 candidates, showed 93 sites with shared polymorphisms; only one of these mutations was found in more than 1% of currently circulating sequences. The minimal diversity found among SARS-CoV-2 sequences can be explained by drift and bottleneck events as the virus spread away from its original epicenter in Wuhan, China. Importantly, there is little evidence that the virus has adapted to its human host since December 2019. Our findings suggest that a single vaccine 10

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Section: Indicators Of Viral Evolution Have Been Shown To Be Robust Pmentioning

confidence: 99%

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

Dearlove

Lewitus

Bai

et al. 2020

Preprint

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“…However, these summary statistics usually do not incorporate tip labels, placing greater emphasis on similarity in tree shapes, and they can be difficult to normalize for comparing pairs of trees with different sizes (Pompei, Loreto, & Tria, 2012). In addition, there are several spectral methods that can be applied to trees by interpreting these objects as graphs (Hendy & Penny, 1993;Lewitus & Morlon, 2015) and the further development of tree distances continues to be an active area of research (Colijn & Plazzotta, 2017;Kendall & Colijn, 2016). It is therefore not feasible to evaluate all possible distances and for our purposes, we have only evaluated a representative subset of distance measures, including commonly used measures such as the RF distance.…”

Section: Discussionmentioning

confidence: 99%

Tree shape‐based approaches for the comparative study of cophylogeny

Avino

et al. 2019

Ecology and Evolution

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Cophylogeny is the congruence of phylogenetic relationships between two different groups of organisms due to their long‐term interaction. We investigated the use of tree shape distance measures to quantify the degree of cophylogeny. We implemented a reverse‐time simulation model of pathogen phylogenies within a fixed host tree, given cospeciation probability, host switching, and pathogen speciation rates. We used this model to evaluate 18 distance measures between host and pathogen trees including two kernel distances that we developed for labeled and unlabeled trees, which use branch lengths and accommodate different size trees. Finally, we used these measures to revisit published cophylogenetic studies, where authors described the observed associations as representing a high or low degree of cophylogeny. Our simulations demonstrated that some measures are more informative than others with respect to specific coevolution parameters especially when these did not assume extreme values. For real datasets, trees’ associations projection revealed clustering of high concordance studies suggesting that investigators are describing it in a consistent way. Our results support the hypothesis that measures can be useful for quantifying cophylogeny. This motivates their usage in the field of coevolution and supports the development of simulation‐based methods, i.e., approximate Bayesian computation, to estimate the underlying coevolutionary parameters.

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“…However, not many such metrics are available. Colijn and Plazzotta (2018) proposed a metric on tree shapes which is the Euclidean norm of the difference between two integer vectors that uniquely describe the two trees. Poon et al (2013) developed a kernel function that measures the similarity between two unlabeled genealogies by accounting for differences in branch lengths and matching number of descendants over all nodes for both trees.…”

Section: Tree Metrics For Comparative Analysismentioning

confidence: 99%

“…The Colijn-Plazzotta (CP) metric. The CP metric is defined on tree shapes (Colijn and Plazzotta, 2018). The CP metric d CP is defined as the Euclidean norm (L 2 -norm) of the difference between two vectors that uniquely describe the two tree shapes.…”

Section: Ranked Tree Shape Summary Statisticsmentioning

confidence: 99%

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A Metric Space of Ranked Tree Shapes and Ranked Genealogies

Kim

Rosenberg

Palacios

2019

Preprint

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Genealogical tree modeling is essential for estimating evolutionary parameters in population genetics and phylogenetics. Recent mathematical results concerning ranked genealogies without leaf labels enable new opportunities in the analysis of evolutionary trees. In particular, comparisons between ranked genealogies facilitate the study of evolutionary processes for organisms sampled in multiple time periods.We propose a metric space on ranked genealogies for lineages sampled from both isochronous and timestamped heterochronous sampling. Our new tree metrics make it possible to conduct statistical analyses of ranked tree shapes and timed ranked tree shapes, or ranked genealogies. Such analyses allow us to assess differences in tree distributions, quantify estimation uncertainty, and summarize tree distributions.We show the utility of our metrics via simulations and an application in infectious diseases.

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A Metric on Phylogenetic Tree Shapes

Cited by 54 publications

References 58 publications

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

Tree shape‐based approaches for the comparative study of cophylogeny

A Metric Space of Ranked Tree Shapes and Ranked Genealogies

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