NDLI: Single-character insertion–deletion model preserves long indels in ancestral sequence reconstruction

Content Provider	Springer Nature : BioMed Central
Author	Jowkar, Gholamhossein Pečerska, Jūlija Gil, Manuel Anisimova, Maria
Abstract	Insertions and deletions (indels) play a significant role in genome evolution across species. Realistic modelling of indel evolution is challenging and is still an open research question. Several attempts have been made to explicitly model multi-character (long) indels, such as TKF92, by relaxing the site independence assumption and introducing fragments. However, these methods are computationally expensive. On the other hand, the Poisson Indel Process (PIP) assumes site independence but allows one to infer single-character indels on the phylogenetic tree, distinguishing insertions from deletions. PIP’s marginal likelihood computation has linear time complexity, enabling ancestral sequence reconstruction (ASR) with indels in linear time. Recently, we developed ARPIP, an ASR method using PIP, capable of inferring indel events with explicit evolutionary interpretations. Here, we investigate the effect of the single-character indel assumption on reconstructed ancestral sequences on mammalian protein orthologs and on simulated data. We show that ARPIP’s ancestral estimates preserve the gap length distribution observed in the input alignment. In mammalian proteins the lengths of inserted segments appear to be substantially longer compared to deleted segments. Further, we confirm the well-established deletion bias observed in real data. To date, ARPIP is the only ancestral reconstruction method that explicitly models insertion and deletion events over time. Given a good quality input alignment, it can capture ancestral long indel events on the phylogeny.
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05986-1.pdf
Ending Page	23
Page Count	23
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/s12859-024-05986-1
Journal	BMC Bioinformatics
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2024-12-02
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Ancestral sequence reconstruction Insertion Deletion Indel pattern Long indel Gap length distribution Mammalian genomics Poisson indel process Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

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