duplicated genes and complex life

 

https://www.the-scientist.com/duplicated-genes-point-to-an-earlier-start-to-complex-life-73824?utm_campaign=5750943-TS_News%20Alerts_2025&utm_medium=email&_hsenc=p2ANqtz-8YeU16fezFsBa86-PcufgjP204myENSvl3cFTX7lKyIApWXgXonHPqAepC0EaS1zXkMAH7dWNqWYqK1Hz8BmHzNDc1SA&_hsmi=396443562&utm_content=396443562&utm_source=hs_email

The provided article highlights a study led by researchers at the University of Bristol that challenges current timelines for the evolution of complex life:

• Earlier Eukaryotic Origins: The study suggests that eukaryotic cells began forming nearly one billion years earlier than previously believed.

• Methodology: Researchers used a "molecular clock" approach by creating a phylogenetic tree from 62 genes across eukaryotes, bacteria, and archaea to estimate evolutionary rates.

• Key Divergence Dates:

  • The archaeal branch leading to the nucleus (nFECA) diverged between 3.05 and 2.79 billion years ago.

  • The bacterial ancestors of mitochondria (mFECA) branched between 2.37 and 2.13 billion years ago.

• Trait Emergence: Tracking more than 100 gene duplication events revealed that many essential eukaryotic traits, such as the cytoskeleton and nucleus, likely emerged before mitochondria were acquired.

• Environmental Context: These results indicate that the archaeal ancestors of eukaryotes were evolving complex features in anoxic oceans roughly a billion years before atmospheric oxygen became abundant.

Based on the study discussed in the article, the following papers are directly related to the research on the evolutionary assembly of eukaryotes and the timing of their origins:

Primary Study

• Dated gene duplications elucidate the evolutionary assembly of eukaryotes (2025)

  • Authors: Christopher J. Kay, Anja Spang, Gergely J. Szöllősi, Davide Pisani, Tom A. Williams, and Philip C. J. Donoghue.

  • Publication: Nature.

  • Core Finding: This study uses a relaxed molecular clock and gene duplication events to show that complex eukaryotic traits (like the nucleus and cytoskeleton) emerged between 3.0 and 2.25 billion years ago, significantly before mitochondrial acquisition.

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Key Related Research

The following papers are frequently cited alongside this work or provide the foundational methodology and competing hypotheses:

• The emerging view on the origin and early evolution of eukaryotic cells (2024)

  • Authors: Julian Vosseberg, Jolien J. E. van Hooff, et al.

  • Publication: Nature.

  • Focus: A recent review and analysis of eukaryogenesis, estimating the domain's emergence between 1.8 and 2.7 billion years ago.

• The nature of the last universal common ancestor and its impact on the early Earth system (2024)

  • Authors: Nina Dombrowski, Philip C. J. Donoghue, et al.

  • Publication: Nature Ecology & Evolution.

  • Focus: Uses a similar "cross-bracing" molecular clock methodology to date LUCA to ~4.2 billion years ago, providing the deep-time context for early life evolution.

• Timing the origin of eukaryotic cellular complexity with ancient duplications (2021)

  • Authors: Julian Vosseberg, Jolien J. E. van Hooff, et al.

  • Publication: Nature Ecology & Evolution.

  • Focus: An earlier phylogenomic study that also utilized gene duplications to infer that the archaeal host already possessed eukaryote-like complexity before engulfing the proto-mitochondrion.

• Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin (2018)

  • Authors: Holly C. Betts, Tom A. Williams, Philip C. J. Donoghue, et al.

  • Publication: Nature Ecology & Evolution.

  • Focus: Establishes a timescale for early life, suggesting modern eukaryotes emerged late (<1.84 Ga), a timeline the 2025 Kay et al. paper significantly revises.

• Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: Eukaryogenesis just made easier? (2015)

  • Author: Eugene V. Koonin.

  • Publication: Philosophical Transactions of the Royal Society B.

  • Focus: A foundational paper discussing the "bursts" of gene gain and the archaeal roots of eukaryotes.

Yes, the duplicated gene data from the study "Dated gene duplications elucidate the evolutionary assembly of eukaryotes" (Kay et al., 2025) is publicly available.

The researchers have deposited the full dataset, including the specific gene families and analysis code, in the University of Bristol's data repository.

Where to Access the Data

• Data Repository Link: The evolutionary assembly of eukaryotes (data.bris).

• Contents: The dataset includes:

  • Gene Family Results: Tables listing the specific gene families that underwent duplications prior to the Last Eukaryotic Common Ancestor (LECA).

  • Species Trees: The time-resolved phylogenetic trees used as the "molecular clock".

  • Analysis Pipelines: The code for domain analysis and the pipelines used to date the duplication events.

What the Data Reveals

The data identifies over 100 gene families with duplications that predated mitochondrial symbiosis. These include genes responsible for:

• Cytoskeleton: Actin and tubulin families originating from archaea.

• Cell Processes: RNA polymerase and the spliceosome.

• Endomembrane System: Genes related to internal transport that reveal origins from distinct bacterial lineages.

This dataset is particularly valuable because it provides the evidence used to "reject mitochondrion-early scenarios" by showing that many complex traits emerged between 3.0 and 2.25 billion years ago.

Would you like me to help you find more specific details on a particular gene family mentioned in the study, such as the Asgard-related cytoskeletal genes?

The dataset associated with the study "Dated gene duplications elucidate the evolutionary assembly of eukaryotes" (Kay et al., 2025) includes the following key figures regarding its species and sequence content:

• Species Tree Marker Genes: The researchers constructed a foundational phylogenetic tree using a representative sample of organisms across the tree of life based on 62 genes.

• Gene Duplication Families: The team identified and analyzed more than 100 gene families that originated in prokaryotes and underwent duplications during eukaryogenesis.

• Time-Resolved Gene Trees: From these families, the study produced a total of 135 time-resolved gene trees.

  • 95 trees were of archaeal origin.

  • 40 trees were of bacterial origin.

• Sequence Scope: The framework is built on hundreds of genetic sequences drawn from diverse biological systems and integrated with the fossil record to calibrate the molecular clock.

While the exact total count of species (taxa) in the final database is not explicitly summarized in a single figure in the press summaries, related work by the same research group (e.g., Dombrowski et al., 2024) has utilized datasets of up to 700 genomes (comprising 350 Archaea and 350 Bacteria) for similar large-scale microbial phylogenies.

You can access the full raw data, including the specific gene family results and species trees, at the University of Bristol's data repository.

 

Note: These data do not seem to be large enough for deep learning based research.