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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.

Yasamin Tabatabaee1, Chao Zhang2, Shayesteh Arasti3

  • 1Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Genome Biology and Evolution
|November 26, 2025
PubMed
Summary
This summary is machine-generated.

CASTLES-Pro accurately estimates species tree branch lengths, even with gene duplication and loss. This new method improves upon existing tools for multi-locus phylogenetic analyses.

Keywords:
branch length estimationgene duplication and losshorizontal gene transferincomplete lineage sortingphylogenomicsspecies trees

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Area of Science:

  • Phylogenetics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic branch lengths are crucial for evolutionary analyses.
  • Gene tree heterogeneity from incomplete lineage sorting, duplication, and loss complicates species tree branch length estimation.
  • Existing methods inadequately address multi-copy gene family trees.

Purpose of the Study:

  • To introduce CASTLES-Pro, an algorithm for estimating species tree branch lengths.
  • To account for gene duplication/loss and incomplete lineage sorting in branch length estimation.
  • To improve upon existing methods like CASTLES for both single-copy and multi-copy gene trees.

Main Methods:

  • Developed the CASTLES-Pro algorithm.
  • Utilized simulation studies to evaluate performance.
  • Compared CASTLES-Pro against alternative methods, including concatenation.

Main Results:

  • CASTLES-Pro demonstrates higher accuracy than existing alternatives.
  • The algorithm mitigates the overestimation of terminal branch lengths common with concatenation.
  • CASTLES-Pro shows relative robustness to horizontal gene transfer.

Conclusions:

  • CASTLES-Pro provides a robust solution for species tree branch length estimation.
  • The method effectively handles gene duplication, loss, and incomplete lineage sorting.
  • CASTLES-Pro represents a significant advancement for multi-locus phylogenetic analyses.