Inferences from tip‐calibrated phylogenies: a review and a practical guide

Rieux, Adrien; Balloux, François

doi:10.1111/mec.13586

Cited by 135 publications

(133 citation statements)

References 106 publications

(226 reference statements)

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“…This clearly indicated that the tip dates were informative and could provide sufficient calibrating information for the analysis (Holt et al. 2012; Rieux and Balloux 2016). The estimated genome wide substitution rate is lower than the estimate for Clostridium difficile (1.88E−7) (He et al.…”

Section: Resultsmentioning

confidence: 99%

“…Root-to-tip distances were extracted from the ML phylogeny using TreeStat v1.2 (Rambaut 2008). The relationship between root-to-tip distances and tip dates (Rieux and Balloux 2016) was determined using linear regression analysis in R v3.2.0 (R Core Team 2015). …”

Section: Methodsmentioning

confidence: 99%

“…This random "null set" of tip-date and sequence correlations was then compared with the substitution rate estimate of the genuine tip-date and sequence correlations (Holt et al. 2012; Rieux and Balloux 2016). …”

Section: Methodsmentioning

confidence: 99%

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Multiple introductions and recent spread of the emerging human pathogen Mycobacterium ulcerans across Africa

et al. 2017

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Buruli ulcer (BU) is an insidious neglected tropical disease. Cases are reported around the world but the rural regions of West and Central Africa are most affected. How BU is transmitted and spreads has remained a mystery, even though the causative agent, Mycobacterium ulcerans, has been known for more than 70 years. Here, using the tools of population genomics, we reconstruct the evolutionary history of M. ulcerans by comparing 165 isolates spanning 48 years and representing 11 endemic countries across Africa. The genetic diversity of African M. ulcerans was found to be restricted due to the bacterium’s slow substitution rate coupled with its relatively recent origin. We identified two specific M. ulcerans lineages within the African continent, and inferred that M. ulcerans lineage Mu_A1 existed in Africa for several hundreds of years, unlike lineage Mu_A2, which was introduced much more recently, approximately during the 19th century. Additionally, we observed that specific M. ulcerans epidemic Mu_A1 clones were introduced during the same time period in the three hydrological basins that were well covered in our panel. The estimated time span of the introduction events coincides with the Neo-imperialism period, during which time the European colonial powers divided the African continent among themselves. Using this temporal association, and in the absence of a known BU reservoir or—vector on the continent, we postulate that the so-called "Scramble for Africa" played a significant role in the spread of the disease across the continent.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Multiple introductions and recent spread of the emerging human pathogen Mycobacterium ulcerans across Africa

et al. 2017

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“…In their recent review, Rieux & Balloux () summarize the current state‐of‐the‐art for tip‐dating, and put forward a ‘how‐to’ guide to perform such analyses. While their review is both comprehensive and timely, we feel the need to elaborate on a consequential element of tip‐dating that received only limited attention.…”

mentioning

confidence: 99%

“…While their review is both comprehensive and timely, we feel the need to elaborate on a consequential element of tip‐dating that received only limited attention. Rieux & Balloux () acknowledge that rate estimates from tip‐dated phylogenies may be upwardly biased under less than simple demographic scenarios, such as structured populations (Navascués & Emerson ). One potential explanation put forward for this bias by Navascués & Emerson () is that population structure may produce trees where ancient DNA (aDNA) and modern DNA (mDNA) segregate in different lineages.…”

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confidence: 99%

Comment on Rieux and Balloux: calibration from tip‐dating can compromise topological accuracy and evolutionary inference

2016

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We contribute to the recent review of Rieux & Balloux, 2016, Mol. Ecol., 25, 1911 on inferences from tip-dated phylogenies by developing their discussion on the influence of population size (N e ) under panmixia for the estimation of substitution rate (l). We highlight how phylogenetic trees inferred with tip-dated sequences under large panmictic N e tend to erroneously enforce an age-based coalescent pattern on the posterior distribution of trees, which in turn results in systematically inflated estimates of l. We discuss the consequences of this and suggest how to accommodate the issue in the short term and long term.

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