e-journal

The effect of genetic structure on molecular dating and tests for temporal signal

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1. ‘Dated-tip’methods ofmolecular dating useDNAsequences sampled at different times, to estimate the age of
their most recent common ancestor. Several tests of ‘temporal signal’ are available to determine whether data sets
are suitable for such analysis.However, it remains unclear whether these tests are reliable.
2. We investigate the performance of several tests of temporal signal, including some recently suggested modifications.
We use simulated data (where the true evolutionary history is known), and whole genomes of methicillin-
resistant Staphylococcus aureus (to show how particular problems arise with real-world data sets).
3. We show that all of the standard tests of temporal signal are seriouslymisleading for data where temporal and
genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at
similar times). This is not an artefact of genetic structure or tree shape per se, and can arise even when sequences
have measurably evolved during the sampling period. More positively, we show that a ‘clustered permutation’
approach introduced by Duch^ene et al. (Molecular Biology and Evolution, 32, 2015, 1895) can successfully correct
for this artefact in all cases and introduce techniques for implementing this method with real data sets.
4. The confounding of temporal and genetic structures may be difficult to avoid in practice, particularly for outbreaks
of infectious disease, or when using ancient DNA. Therefore, we recommend the use of ‘clustered permutation’
for all analyses. The failure of the standard tests may explain why different methods of dating pathogen
origins have reached such wildly different conclusions.

Key-words: Bayesian dating, dated-tips, pathogen origins, permutation tests, Staphylococcus
aureus

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Informasi Detail

Judul Seri

Methods in Ecology and Evolution

No. Panggil

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Penerbit

: John Wiley & Sons., 2016

Deskripsi Fisik

Methods in Ecology and Evolution 2016, 7, 80–89

Bahasa

English

ISBN/ISSN

doi: 10.1111/2041-21

Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

Bilogi

Info Detail Spesifik

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Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

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