ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

ClockstaRX : Testing Molecular Clock Hypotheses With Genomic Data. / Duchêne, David A.; Duchêne, Sebastián; Stiller, Josefin; Heller, Rasmus; Ho, Simon Y. W.

In: Genome Biology and Evolution, Vol. 16, No. 4, evae064, 2024.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Duchêne, DA, Duchêne, S, Stiller, J, Heller, R & Ho, SYW 2024, 'ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data', Genome Biology and Evolution, vol. 16, no. 4, evae064. https://doi.org/10.1093/gbe/evae064

APA

Duchêne, D. A., Duchêne, S., Stiller, J., Heller, R., & Ho, S. Y. W. (2024). ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data. Genome Biology and Evolution, 16(4), [evae064]. https://doi.org/10.1093/gbe/evae064

Vancouver

Duchêne DA, Duchêne S, Stiller J, Heller R, Ho SYW. ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data. Genome Biology and Evolution. 2024;16(4). evae064. https://doi.org/10.1093/gbe/evae064

Author

Duchêne, David A. ; Duchêne, Sebastián ; Stiller, Josefin ; Heller, Rasmus ; Ho, Simon Y. W. / ClockstaRX : Testing Molecular Clock Hypotheses With Genomic Data. In: Genome Biology and Evolution. 2024 ; Vol. 16, No. 4.

Bibtex

@article{6592cb5154054b97bb6c7ab1ea8ddb61,
title = "ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data",
abstract = "Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests for identifying groups of loci and branches that make a large contribution to patterns of rate variation. This information can then be used to test for drivers of genomic evolutionary rates or to inform models for molecular dating. Drawing on the results of a simulation study, we recommend forms of data exploration and filtering that might be useful prior to molecular-clock analyses.",
author = "Duch{\^e}ne, {David A.} and Sebasti{\'a}n Duch{\^e}ne and Josefin Stiller and Rasmus Heller and Ho, {Simon Y. W.}",
year = "2024",
doi = "10.1093/gbe/evae064",
language = "English",
volume = "16",
journal = "Genome Biology and Evolution",
issn = "1759-6653",
publisher = "Oxford University Press",
number = "4",

}

RIS

TY - JOUR

T1 - ClockstaRX

T2 - Testing Molecular Clock Hypotheses With Genomic Data

AU - Duchêne, David A.

AU - Duchêne, Sebastián

AU - Stiller, Josefin

AU - Heller, Rasmus

AU - Ho, Simon Y. W.

PY - 2024

Y1 - 2024

N2 - Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests for identifying groups of loci and branches that make a large contribution to patterns of rate variation. This information can then be used to test for drivers of genomic evolutionary rates or to inform models for molecular dating. Drawing on the results of a simulation study, we recommend forms of data exploration and filtering that might be useful prior to molecular-clock analyses.

AB - Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests for identifying groups of loci and branches that make a large contribution to patterns of rate variation. This information can then be used to test for drivers of genomic evolutionary rates or to inform models for molecular dating. Drawing on the results of a simulation study, we recommend forms of data exploration and filtering that might be useful prior to molecular-clock analyses.

U2 - 10.1093/gbe/evae064

DO - 10.1093/gbe/evae064

M3 - Journal article

C2 - 38526019

VL - 16

JO - Genome Biology and Evolution

JF - Genome Biology and Evolution

SN - 1759-6653

IS - 4

M1 - evae064

ER -

ID: 386936692