PCI Paleontology

220

Title *

PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteinsuse asterix (*) to get italics

Authors *

Ioannis Patramanis, Jazmín Ramos-Madrigal, Enrico Cappellini, Fernando RacimoPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2023

Picture *

Abstract *

<p>Ancient proteins from fossilized or semi-fossilized remains can yield phylogenetic information at broad temporal horizons, in some cases even millions of years into the past. In recent years, peptides extracted from archaic hominins and long-extinct mega-fauna have enabled unprecedented insights into their evolutionary history. In contrast to the field of ancient DNA - where several computational methods exist to process and analyze sequencing data - few tools exist for handling ancient protein sequence data. Instead, most studies rely on loosely combined custom scripts, which makes it difficult to reproduce results or share methodologies across research groups. Here, we present PaleoProPhyler: a new fully reproducible pipeline for aligning ancient peptide data and subsequently performing phylogenetic analyses. The pipeline can not only process various forms of proteomic data, but also easily harness genetic data in different formats (CRAM, BAM, VCF) and translate it, allowing the user to create reference panels for phyloproteomic analyses. We describe the various steps of the pipeline and its many functionalities, and provide some examples of how to use it. PaleoProPhyler allows researchers with little bioinformatics experience to efficiently analyze palaeoproteomic sequences, so as to derive insights from this valuable source of evolutionary data.</p>

Indicate the full web address (DOI or URL) giving public access to these data (if you have any problems with the deposit of your data, please contact contact@paleo.peercommunityin.org). In case all raw data are included in the preprint, indicate the DOI or URL of the preprint. *

https://doi.org/10.5281/zenodo.7728060You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

Indicate the full web address (DOI or URL) giving public access to these scripts (if you have any problems with the deposit of your scripts, please contact contact@paleo.peercommunityin.org). In case all raw scripts are included in the preprint, indicate the DOI or URL of the preprint. *

https://github.com/johnpatramanis/Proteomic_PipelineYou should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

Indicate the full web address (DOI, SWHID or URL) giving public access to these codes (if you have any problems with the deposit of your codes, please contact contact@paleo.peercommunityin.org). In case all raw codes are included in the preprint, indicate the DOI or URL of the preprint. *

https://github.com/johnpatramanis/Proteomic_PipelineYou should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Keywords (optional)

Pipeline, Workflow, Palaeoproteomics, Paleoproteomics, Phylogenetics, Phyloproteomics, Hominid evolution , Human evolution

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

Evolutionary biology, Paleoanthropology, Paleogenetics & Ancient DNA, Phylogenetics

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

e.g. John Doe john@doe.com

No need for them to be recommenders of PCIPaleo. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

Opposed reviewers - Suggest up to 5 people not to invite as reviewers. (Optional)

e.g. John Doe john@doe.com

Submission date

2023-02-24 13:40:12

Recommender

Leslea Hlusko

Reviewers

or Register
Submit a preprint

MANAGING BOARD

MEMBER OF

INDEXED BY