Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
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...
5.7K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.1K
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...
7.1K
Phylogenetic Trees03:21

Phylogenetic Trees

45.3K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.3K
What is Population Genetics?01:25

What is Population Genetics?

57.8K
A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
57.8K
Next-generation Sequencing03:00

Next-generation Sequencing

88.5K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
88.5K
RNA-seq03:21

RNA-seq

9.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping.

Genetics·2026
Same author

Deep learning reveals genomic regions introgressed between two recurrently hybridizing lynx species.

Molecular biology and evolution·2026
Same author

Soft Selective Sweeps Predominate in the Yellow Fever Mosquito Aedes aegypti.

Molecular biology and evolution·2026
Same author

Recombination and the role of pseudo-overdominance in polyploid evolution.

G3 (Bethesda, Md.)·2026
Same author

INTERPRETING CONVOLUTIONAL NEURAL NETWORKS IN POPULATION GENETICS.

bioRxiv : the preprint server for biology·2025
Same author

The contribution of transposable element insertions to genetic diversity in <i>Aedes aegypti</i> populations.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: Jun 15, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.1K

Tree sequences as a general-purpose tool for population genetic inference.

Logan S Whitehouse1, Dylan Ray1, Daniel R Schrider1

  • 1Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA, 120 Mason Farm Rd, Chapel Hill, NC 27514.

Biorxiv : the Preprint Server for Biology
|August 26, 2024
PubMed
Summary

This study introduces a graph convolutional network (GCN) to analyze tree sequences, a new genetic data format. This method efficiently infers population genetics parameters, matching or surpassing existing convolutional neural network (CNN) approaches.

Keywords:
ancestral recombination graphsdemographic inferenceintrogressionrecombination rate estimationselective sweepstree sequences

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.3K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

15.8K

Related Experiment Videos

Last Updated: Jun 15, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.1K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.3K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

15.8K

Area of Science:

  • Population genetics
  • Bioinformatics
  • Machine learning in genomics

Background:

  • Increasing population genetics data necessitates efficient storage and analysis methods like tree sequences.
  • Existing neural network methods often require converting tree sequences to alignment formats, losing efficiency.

Purpose of the Study:

  • To develop a Graph Convolutional Network (GCN) for direct analysis of tree sequence data.
  • To enable neural network applications on tree sequences without format conversion.
  • To evaluate GCN performance against Convolutional Neural Networks (CNNs) on population genetics tasks.

Main Methods:

  • Implementation of a Graph Convolutional Network (GCN) model.
  • Direct learning from tree sequence topology and node data.
  • Benchmarking against CNNs on tasks like recombination rate estimation, selection detection, introgression detection, and demographic inference.

Main Results:

  • The GCN approach successfully learns directly from tree sequences.
  • Performance on population genetics inference tasks was comparable or superior to CNN-based methods.
  • Demonstrated the utility of GCNs for analyzing novel tree sequence data structures.

Conclusions:

  • Graph convolutional networks offer an efficient and effective method for population genetics inference using tree sequences.
  • This work provides a foundation for future developments in analyzing large-scale genetic data.
  • Direct analysis of tree sequences with GCNs streamlines population genetics research.