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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

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Published on: May 28, 2021

Basal jawed vertebrate phylogenomics using transcriptomic data from Solexa sequencing.

Ming Chen1, Ming Zou, Lei Yang

  • 1Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.

Plos One
|May 5, 2012
PubMed
Summary
This summary is machine-generated.

This study reconstructs jawed vertebrate relationships using phylogenomic data, supporting traditional classifications over mitochondrial sequence analyses. Divergence times align with fossil records, clarifying vertebrate evolutionary history.

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Published on: January 25, 2019

Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Genomics

Background:

  • Molecular phylogenetic analyses using mitochondrial DNA have challenged traditional classifications of basal jawed vertebrates.
  • Previous studies proposed a split into tetrapods and a piscine group, with lungfish and bichir at the base.

Purpose of the Study:

  • To reconstruct the phylogenetic tree of basal jawed vertebrates using transcriptomic and genomic data.
  • To estimate divergence times and resolve conflicting phylogenetic relationships.

Main Methods:

  • Generated transcriptomes for an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.).
  • Utilized public databases for expressed sequences and whole genome sequences.
  • Reconstructed the phylogenetic tree using 111 genes and estimated divergence times.

Main Results:

  • The phylogenomic study supports the traditional classification of gnathostomes into Chondrichthyes and Osteichthyes.
  • Lungfish and tetrapods form a monophyletic group, and bichir groups with teleost species.
  • Mitochondrial data-based trees were rejected by the approximately unbiased test (p = 0).
  • Estimated divergence times align with the fossil record.

Conclusions:

  • Phylogenomic analysis successfully resolved basal jawed vertebrate relationships, confirming traditional classifications.
  • The study highlights the importance of using comprehensive genomic data for accurate phylogenetic reconstruction.
  • Divergence time estimates provide valuable insights into vertebrate evolution.