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Updated: May 16, 2025

Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers MADM
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Genomic evolution reshapes cell-type diversification in the amniote brain.

Duoyuan Chen1, Zhenkun Zhuang2, Maolin Huang3

  • 1BGI Research, Hangzhou 310030, China; BGI Research, Shenzhen 518083, China; Key Laboratory of Spatial Omics of Zhejiang Province, BGI Research, Hangzhou 310030, China; State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Hangzhou 310030, China.

Developmental Cell
|May 14, 2025
PubMed
Summary

This study reveals evolutionary brain differences in amniotes by creating a large single-cell atlas. Key findings include bird-specific cell types and gene expression patterns linked to adaptation.

Keywords:
amniotebrain sciencecerebellumevolution of cell typessingle-nucleus RNA-seqtelencephalon

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Area of Science:

  • Evolutionary biology
  • Neuroscience
  • Genomics

Background:

  • Amniotes evolved complex brains and cognition over 320 million years.
  • Genetic and gene expression mechanisms underlying these changes remain largely unexplored.

Purpose of the Study:

  • To create a comprehensive single-cell atlas of the amniote telencephalon and cerebellum.
  • To identify species-specific variations, conservation, and diversification of cell types across evolution.
  • To investigate genetic mechanisms driving brain evolution and adaptation.

Main Methods:

  • Generated a single-cell atlas of over 1.3 million cells from turtles, birds (zebra finches, pigeons), mice, and macaques.
  • Utilized single-cell resolution spatial transcriptomics to analyze gene expression patterns.
  • Performed comparative analysis of cell types and gene expression across species.

Main Results:

  • Identified significant species-specific variations in telencephalon excitatory neurons (EXs) and cerebellar cell types.
  • Observed distinct gene expression patterns (SLC17A6 vs. SLC17A7) in bird and mammal EXs.
  • Discovered a bird-specific Purkinje cell subtype (SVIL+) linked to the KDM1A pathway and positively selected genes.

Conclusions:

  • Species-specific cell types and gene expression contribute to amniote brain evolution and cognitive diversity.
  • The KDM1A pathway and positively selected genes in bird Purkinje cells suggest evolutionary optimization for adaptation.
  • Genetic diversification plays a crucial role in developing specialized cell types for ecological and behavioral adaptation.