# Data

Policy information about [availability of data](#)

All manuscripts must include a [data availability statement](#). This statement should provide the following information, where applicable:

- Accession codes, unique identifiers, or web links for publicly available datasets

- A description of any restrictions on data availability

- For clinical datasets or third party data, please ensure that the statement adheres to our [policy](#)

All raw DNA sequence data generated for this study are deposited in the European Nucleotide Archive under the following bioprojects PRJNA478314, PRJEB35285, PRJEB49212 and PRJNA678873. All analysed data and metadata are available in Zenodo (https://doi.org/10.5281/zenodo.10778206). The resulting trees and metadata are also available in GBIF (https://doi.org/10.15468/4njn8b) and Open Tree of Life (https://tree.opentreeoflife.org/curator/study/view/ot_2304). The names used in this work match the World Checklist of Vascular Plants (https://doi.org/10.34885/jdh2-dr22).

# Research involving human participants, their data, or biological material

Policy information about studies with [human participants or human data](#). See also policy information about [sex, gender (identity/presentation), and sexual orientation](#) and [race, ethnicity and racism](#).

Reporting on sex and gender Not applicable

Reporting on race, ethnicity, or other socially relevant groupings Not applicable

Population characteristics Not applicable

Recruitment Not applicable

Ethics oversight Not applicable

Note that full information on the approval of the study protocol must also be provided in the manuscript.

# Field-specific reporting

Please select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before making your selection.

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Life sciences

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Behavioural & social sciences

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Ecological, evolutionary & environmental sciences

For a reference copy of the document with all sections, see [nature.com/documents/nr-reporting-summary-flat.pdf](https://nature.com/documents/nr-reporting-summary-flat.pdf)

# Ecological, evolutionary & environmental sciences study design

All studies must disclose on these points even when the disclosure is negative.

Study description We sampled nearly 8,000 genera and 353 genes to infer a phylogenetic tree for angiosperms, dated and calibrated it with a dataset of 200 fossils, and used this evolutionary time frame to study the diversification of the group.

Research sample We aimed to produce a dataset with at least one species per genus for >50% of the ca. 13,600 currently angiosperms genera. For genera with multiple species available, we retained up to three species, selecting primarily by phylogenetic representation followed by amount of data (number of genes and total length of recovery). Twelve species of gymnosperms were used as outgroups, one from each family. The final dataset contains 9,506 species, 7,923 genera, 416 families and 64 orders of angiosperms. It comprises 7,561 samples with data produced by this project and 1,963 samples mined from public repositories.

Sampling strategy We sourced samples from herbarium, living, DNA bank and tissue bank collections.

Data collection We produced target sequence capture data using the Angiosperms353 probe kit. Total DNA was extracted using CTAB protocol and quantified by fluorometry. Average fragment size was assessed with 1% agarose gel. DNA extracts were diluted to 4 ng/ul. For extracts with high molecular weight, total DNA was fragmented using Covaris M220 Focused ultrasonicator. Genomic DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit, following manufacturer's protocol at half volume, and with dual indexing. Libraries were normalised to 10 nM and pooled in equimolar amounts according to the average fragment size and taxonomic groups. Pools included, on average, 20-24 libraries. The pools were hybridised with Angiosperms353 probe kit. Hybridised pools were normalised to 7nM and combined for sequencing. Sequencing was carried out in Illumina platforms MiSeq and HiSeq.

Timing and spatial scale Data production started in May 2016 and ended in December 2021.

Data exclusions We excluded samples that failed both phylogenetic and barcode validation, as described in Baker (2022). Syst. Biol. 71: 301-319. We
Data exclusions

also excluded samples if more than three accessions were available for the same genus.

Reproducibility

All raw data and intermediate files are provided, making every step reproducible. All accessions used are listed in the Supplementary Table 1.

Randomization

Not applicable - randomization was not required.

Blinding

Not applicable - this work does not involve trials or controlled experiments.

Did the study involve field work?

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Yes

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No

Reporting for specific materials, systems and methods

We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material, system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.

Materials & experimental systems

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Methods

<figure><img src="image_30.png" /></figure>
Data exclusions

also excluded samples if more than three accessions were available for the same genus.

Reproducibility

All raw data and intermediate files are provided, making every step reproducible. All accessions used are listed in the Supplementary Table 1.

Randomization

Not applicable - randomization was not required.

Blinding

Not applicable - this work does not involve trials or controlled experiments.

Did the study involve field work?

<figure><img src="image_20.png" /></figure>

Yes

<figure><img src="image_21.png" /></figure>

No

Reporting for specific materials, systems and methods

We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material, system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.

Materials & experimental systems

<figure><img src="image_22.png" /></figure>

Methods

<figure><img src="image_23.png" /></figure>