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Updated: Jun 6, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction.

Gholamhossein Jowkar^1,2,3, Jūlija Pečerska^4,5, Manuel Gil^4,5

¹Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Neuchâtel, Switzerland. xjok@zhaw.ch.

BMC Bioinformatics

|December 1, 2024

Summary

ARPIP, an ancestral sequence reconstruction method, accurately models insertion and deletion (indel) events. It preserves indel length distributions and captures long indel events, outperforming previous methods.

Keywords:

Ancestral sequence reconstruction Deletion Gap length distribution Indel pattern Insertion Long indel Mammalian genomics Poisson indel process

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Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

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Published on: September 3, 2009

Area of Science:

Genomics
Computational Biology
Evolutionary Biology

Background:

Insertions and deletions (indels) are crucial for genome evolution but challenging to model accurately.
Existing methods for modeling long indels are computationally intensive.
The Poisson Indel Process (PIP) allows efficient inference of single-character indels and ancestral sequence reconstruction (ASR).

Purpose of the Study:

To investigate the impact of the single-character indel assumption in ASR.
To evaluate the ARPIP method's ability to reconstruct ancestral sequences with indels.
To analyze indel length distributions and biases in mammalian protein orthologs.

Main Methods:

Utilized the ARPIP method, based on the Poisson Indel Process (PIP).
Applied ARPIP to mammalian protein orthologs and simulated datasets.
Analyzed reconstructed ancestral sequences for gap length distribution and indel characteristics.

Main Results:

ARPIP ancestral estimates successfully preserve the gap length distribution from input alignments.
Mammalian protein data shows inserted segments are significantly longer than deleted segments.
The study confirms a known deletion bias in real biological data.
ARPIP demonstrates capability in capturing ancestral long indel events.

Conclusions:

ARPIP is a unique ASR method that explicitly models indel events over time.
The single-character indel assumption in ARPIP is effective for reconstructing ancestral sequences.
ARPIP provides evolutionary insights into indel processes, especially in mammalian protein evolution.