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Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

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.
In contrast, regions which code...

Gene Evolution - Fast or Slow?

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Convergent Evolution

Convergent Evolution

Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.

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SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution.

B C Haller¹, C W Nelson^2,3, M F Rodrigues⁴

¹Dept. of Computational Biology, Cornell University, Ithaca, NY 14850, USA.

Biorxiv : the Preprint Server for Biology

|September 15, 2025

Summary

Researchers developed a new SLiM 5 model to simulate the entire human genome's molecular evolution. This tool, "SimHumanity," aids in testing hypotheses about human evolutionary history, including migration and admixture events.

Keywords:

SLiM agent-based model forward genetic simulation full genome simulation human evolution individual-based model sex chromosome evolution whole genome simulation

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Area of Science:

Evolutionary biology
Computational genomics
Human origins

Background:

Reconstructing human evolutionary history relies on methodological advancements, with genetic and genomic data being crucial.
Genetic simulations are vital for testing hypotheses on human migration and admixture with archaic hominins.
Previous whole-genome simulations were challenging due to limitations in evolutionary simulation frameworks.

Purpose of the Study:

To introduce a novel, open-source SLiM 5 model for simulating the molecular evolution of the complete human genome.
To provide a customizable and reusable tool for researchers in human evolutionary studies.
To facilitate advanced simulations of human evolutionary dynamics at a whole-genome scale.

Main Methods:

Development of three versions of a SLiM 5-based model for whole-genome human evolutionary simulations.
Utilizing SLiM 5's capabilities to model complex demographic scenarios and evolutionary dynamics.
Demonstrating the model's utility through simple analyses of simulation results.

Main Results:

Successful construction of SLiM 5 models enabling whole-genome simulations of human evolution.
Demonstrated ease of simulating humans at a whole-genome scale under various demographic models.
Provided illustrative analyses showcasing the model's application and potential.

Conclusions:

The developed SLiM 5 model,
SimHumanity
, simplifies whole-genome simulations of human molecular evolution.
This open-source tool is expected to advance research in human evolutionary simulations.
Facilitates testing of hypotheses related to human migration, admixture, and evolutionary dynamics.