An Integrated Method to Reconstruct Ancient Proteins.

Amanda K Garcia, Evrim Fer, Cathryn Sephus, Betul Kacar

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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

4 authors.

Amanda K GarciaDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.

Evrim FerDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.

Cathryn SephusScripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA.

Betul KacarDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA. bkacar@wisc.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Proteins have played a fundamental role throughout life's history on Earth. Despite their biological importance, ancient origin, early function, and evolution of proteins are seldom able to be directly studied because few of these attributes are preserved across geologic timescales. Ancestral sequence reconstruction (ASR) provides a method to infer ancestral amino acid sequences and determine the evolutionary predecessors of modern-day proteins using phylogenetic tools. Laboratory application of ASR allows ancient sequences to be deduced from genetic information available in extant organisms and then experimentally resurrected to elucidate ancestral characteristics. In this article, we provide a generalized, stepwise protocol that considers the major elements of a well-designed ASR study and details potential sources of reconstruction bias that can reduce the relevance of historical inferences. We underscore key stages in our approach so that it may be broadly utilized to reconstruct the evolutionary histories of proteins.

Indexed as

Evolution, MolecularProteinsAmino Acid SequencePhylogenyProteinsAncestral sequence reconstructionAncestral sequence uncertaintyMaximum likelihoodMolecular paleobiologyPhylogenetic reconstruction

Identifiers

PMID36083453

DOI10.1007/978-1-0716-2691-7_13

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.