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Measuring Asymmetry in Time-Stamped Phylogenies.

Dearlove BL, Frost SD - PLoS Comput. Biol. (2015)

Bottom Line: We present a simple permutation-based approach for testing for asymmetry in a phylogeny, where we compare the observed phylogeny with random phylogenies with the same sampling and coalescence times, to reduce the false positive rate.We also demonstrate how profiles of measures of asymmetry calculated over a range of evolutionary times in the phylogeny can be used to identify local asymmetry.In combination with different metrics of asymmetry, this combined approach offers detailed insights of how phylogenies reconstructed from real viral datasets may deviate from the simplistic assumptions of commonly used coalescent and birth-death process models.

View Article: PubMed Central - PubMed

Affiliation: Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.

ABSTRACT
Previous work has shown that asymmetry in viral phylogenies may be indicative of heterogeneity in transmission, for example due to acute HIV infection or the presence of 'core groups' with higher contact rates. Hence, evidence of asymmetry may provide clues to underlying population structure, even when direct information on, for example, stage of infection or contact rates, are missing. However, current tests of phylogenetic asymmetry (a) suffer from false positives when the tips of the phylogeny are sampled at different times and (b) only test for global asymmetry, and hence suffer from false negatives when asymmetry is localised to part of a phylogeny. We present a simple permutation-based approach for testing for asymmetry in a phylogeny, where we compare the observed phylogeny with random phylogenies with the same sampling and coalescence times, to reduce the false positive rate. We also demonstrate how profiles of measures of asymmetry calculated over a range of evolutionary times in the phylogeny can be used to identify local asymmetry. In combination with different metrics of asymmetry, this combined approach offers detailed insights of how phylogenies reconstructed from real viral datasets may deviate from the simplistic assumptions of commonly used coalescent and birth-death process models.

No MeSH data available.


Related in: MedlinePlus

Permuting a time-stamped tree.The times of the tips (solid blue lines) and internal nodes (dashed blue lines) from the observed tree (top, black) are preserved in the permuted tree (bottom, dark grey).
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pcbi.1004312.g002: Permuting a time-stamped tree.The times of the tips (solid blue lines) and internal nodes (dashed blue lines) from the observed tree (top, black) are preserved in the permuted tree (bottom, dark grey).

Mentions: To obtain the distribution of possible values for each the statistics for an observed tree, we permute the tree whilst retaining the same tip sampling and internal node times (Fig 2). These simulated trees form a neutrally evolving distribution of coalescent trees, conditioned on the same tip and internal node times as the observed tree.


Measuring Asymmetry in Time-Stamped Phylogenies.

Dearlove BL, Frost SD - PLoS Comput. Biol. (2015)

Permuting a time-stamped tree.The times of the tips (solid blue lines) and internal nodes (dashed blue lines) from the observed tree (top, black) are preserved in the permuted tree (bottom, dark grey).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492995&req=5

pcbi.1004312.g002: Permuting a time-stamped tree.The times of the tips (solid blue lines) and internal nodes (dashed blue lines) from the observed tree (top, black) are preserved in the permuted tree (bottom, dark grey).
Mentions: To obtain the distribution of possible values for each the statistics for an observed tree, we permute the tree whilst retaining the same tip sampling and internal node times (Fig 2). These simulated trees form a neutrally evolving distribution of coalescent trees, conditioned on the same tip and internal node times as the observed tree.

Bottom Line: We present a simple permutation-based approach for testing for asymmetry in a phylogeny, where we compare the observed phylogeny with random phylogenies with the same sampling and coalescence times, to reduce the false positive rate.We also demonstrate how profiles of measures of asymmetry calculated over a range of evolutionary times in the phylogeny can be used to identify local asymmetry.In combination with different metrics of asymmetry, this combined approach offers detailed insights of how phylogenies reconstructed from real viral datasets may deviate from the simplistic assumptions of commonly used coalescent and birth-death process models.

View Article: PubMed Central - PubMed

Affiliation: Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.

ABSTRACT
Previous work has shown that asymmetry in viral phylogenies may be indicative of heterogeneity in transmission, for example due to acute HIV infection or the presence of 'core groups' with higher contact rates. Hence, evidence of asymmetry may provide clues to underlying population structure, even when direct information on, for example, stage of infection or contact rates, are missing. However, current tests of phylogenetic asymmetry (a) suffer from false positives when the tips of the phylogeny are sampled at different times and (b) only test for global asymmetry, and hence suffer from false negatives when asymmetry is localised to part of a phylogeny. We present a simple permutation-based approach for testing for asymmetry in a phylogeny, where we compare the observed phylogeny with random phylogenies with the same sampling and coalescence times, to reduce the false positive rate. We also demonstrate how profiles of measures of asymmetry calculated over a range of evolutionary times in the phylogeny can be used to identify local asymmetry. In combination with different metrics of asymmetry, this combined approach offers detailed insights of how phylogenies reconstructed from real viral datasets may deviate from the simplistic assumptions of commonly used coalescent and birth-death process models.

No MeSH data available.


Related in: MedlinePlus