A new method for inferring timetrees from temporally sampled molecular sequences

Sayaka Miura; Koichiro Tamura; Qiqing Tao; Louise A. Huuki; Sergei L. Kosakovsky Pond; Jessica Priest; Jiamin Deng; Sudhir Kumar

doi:10.1371/journal.pcbi.1007046

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Open Access

Peer-reviewed

Research Article

A new method for inferring timetrees from temporally sampled molecular sequences

Sayaka Miura ,

Contributed equally to this work with: Sayaka Miura, Koichiro Tamura

Roles Data curation, Formal analysis, Investigation, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliations Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America, Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America

http://orcid.org/0000-0001-9881-2848

⨯
Koichiro Tamura ,

Contributed equally to this work with: Sayaka Miura, Koichiro Tamura

Roles Methodology

Affiliations Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan, Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
⨯
Qiqing Tao,

Roles Data curation, Formal analysis, Investigation, Resources, Validation, Writing – review & editing

Affiliations Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America, Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America

http://orcid.org/0000-0001-7360-409X

⨯
Louise A. Huuki,

Roles Formal analysis, Investigation, Visualization

Affiliations Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America, Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
⨯
Sergei L. Kosakovsky Pond,

Roles Writing – review & editing

Affiliations Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America, Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
⨯
Jessica Priest,

Roles Data curation, Formal analysis, Investigation

Affiliations Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America, Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America

http://orcid.org/0000-0001-7511-6284

⨯
Jiamin Deng,

Roles Formal analysis, Investigation, Visualization

Affiliations Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America, Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America

http://orcid.org/0000-0003-0566-4597

⨯
Sudhir Kumar

Roles Conceptualization, Funding acquisition, Methodology, Project administration, Software, Supervision, Validation, Writing – original draft, Writing – review & editing

* E-mail: s.kumar@temple.edu

Affiliations Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America, Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America, Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia

http://orcid.org/0000-0002-9918-8212

⨯

A new method for inferring timetrees from temporally sampled molecular sequences

Sayaka Miura,
Koichiro Tamura,
Qiqing Tao,
Louise A. Huuki,
Sergei L. Kosakovsky Pond,
Jessica Priest,
Jiamin Deng,
Sudhir Kumar

Published: January 17, 2020
https://doi.org/10.1371/journal.pcbi.1007046

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treedater

Posted by evolz on 23 Jan 2020 at 16:52 GMT

The finding that treedater is not robust to autocorrelated rates is much appreciated. I have reproduced this finding using the latest version of treedater. However I would also note that
1) the distribution of errors is highly skewed,
2) the median error in ABR scenarios is closer to the other methods,
3) in a real analysis, the outlying rates would likely raise red flags. I find that most of the error can be resolved by using the 'meanRateLimits' option in treedater. Constraining the value to within 2x of the true rate gives much better results.

No competing interests declared.

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A new method for inferring timetrees from temporally sampled molecular sequences

A new method for inferring timetrees from temporally sampled molecular sequences

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treedater

Posted by evolz on 23 Jan 2020 at 16:52 GMT