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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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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Gene Evolution - Fast or Slow?02:05

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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.
In contrast, regions which code...
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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Synteny and Evolution02:31

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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
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Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
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Multi-species Conserved Sequences02:51

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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Related Experiment Video

Updated: Oct 14, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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pyRSD-CoEv: A python package for selective sweep detection and co-evolutionary gene cluster identification.

Xingxing Zhu1, Haoyu Zhang1, Qianzi Tang1

  • 1Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.

Animal Genetics
|November 3, 2021
PubMed
Summary
This summary is machine-generated.

Identifying genes that coevolve or undergo selective sweeps is crucial for understanding complex traits. The new pyRSD-CoEv package enables this analysis for closely related individuals, addressing a gap in current computational methods.

Keywords:
gene clustershigh-performance computingselective sweep

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Genes interact and coevolve, influencing complex phenotypic traits.
  • Identifying genes under selective sweeps and coevolution is vital.
  • Existing computational methods are limited to closely related breeds or distinct species, lacking approaches for non-replicate individuals.

Purpose of the Study:

  • To introduce pyRSD-CoEv, a novel open-source software package.
  • To enable the identification of genes undergoing coevolution and/or selection-based sweeps.
  • To provide a tool specifically designed for closely related individuals without replicates.

Main Methods:

  • The pyRSD-CoEv package offers two primary analysis workflows for genomic variant data.
  • Workflow 1: Identification of selective sweeps using relative homozygous single nucleotide variant density (RSD).
  • Workflow 2: Identification of coevolutionary gene clusters based on correlated evolutionary rates.

Main Results:

  • Presents pyRSD-CoEv, a free, powerful, open-source Python package (Python 3.7).
  • The package facilitates the analysis of genomic variant data to detect selective sweeps and coevolution.
  • pyRSD-CoEv is available on GitHub and runs on Linux.

Conclusions:

  • pyRSD-CoEv addresses a critical need for analyzing coevolution and selection in closely related, non-replicate individuals.
  • The package provides valuable tools for researchers in evolutionary genetics and genomics.
  • This software enhances our ability to study the genetic basis of complex traits.