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Congruence test of molecular clock calibration hypotheses based on Bayes factor comparisons

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1. Molecular clock calibration is a crucial step for placing phylogenetic trees in the temporal framework required
to test evolutionary hypotheses and estimate evolutionary rates. In general, most authors agree that the best
approach is to incorporate multiple calibrations to avoid the risk of bias associated with a single dating source.
However, the indiscriminate inclusion of as many calibration points as possible can lead to tree shape distortion
and an overestimation of the variation in evolutionary rates among branches due to errors in the geological, paleontological or paleogeographic information used for dating.
2. We present a test of congruence among calibration hypotheses to assist their filtering prior to molecular clock
analysis, which we have called Bayes Factor Cluster Analysis (BFCA). This is a heuristic method based on the
comparison of pairwise calibrations hypotheses by Bayes factors that allows identifying sets of congruent calibrations.
3. We have tested BFCA through simulation using BEAST and MCMCTree programs and analysed a real case of
multiple calibration hypotheses to date the evolution of the genus Carabus (Coleoptera: Carabidae).
4. The analyses of simulated data showed the predictability of change in Bayes factors when comparing alternative
calibration hypotheses on a particular tree topology, and thus the suitability of BFCA in identifying unreliable
calibrations, especially in cases with limited variation in evolutionary rates among branches. The exclusion
of inconsistent calibrations as identified by BFCA produced significant changes in the estimation of divergence
times and evolutionary rates in the genus Carabus, illustrating the importance of filtering calibrations before
analyses.
5. Themethod has been implemented in an open-sourceRpackage called bfca to simplify its application.
Key-words: molecular clock, Bayes factors, calibration hypotheses, Bayes Factor Cluster Analysis,
substitution rate

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Informasi Detail

Judul Seri

Methods in Ecology and Evolution

No. Panggil

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Penerbit

: British Ecological Society., 2014

Deskripsi Fisik

Methods in Ecology and Evolution 2014, 5, 226–242

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

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

Lampiran Berkas

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