Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

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...

Gene Duplication and Divergence

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...

Mutation, Gene Flow, and Genetic Drift

Mutation, Gene Flow, and Genetic Drift

In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).

Multi-species Conserved Sequences

Multi-species Conserved Sequences

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...

What is Population Genetics?

What is Population Genetics?

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.

Applications of Molecular Taxonomy

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

You might also read

Related Articles

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

Sort by

Same author

Genetic predictions of eye and hair colour in the Danish population.

Forensic science international. Genetics·2025

Same author

Bayesian inference of admixture graphs on Native American and Arctic populations.

PLoS genetics·2023

Same author

Author Correction: Comparative and demographic analysis of orang-utan genomes.

Nature·2022

Same author

Insights into bear evolution from a Pleistocene polar bear genome.

Proceedings of the National Academy of Sciences of the United States of America·2022

Same author

Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components.

Molecular biology and evolution·2021

Same author

Targeted conservation genetics of the endangered chimpanzee.

Heredity·2020

Search research articles

Related Experiment Video

Updated: Apr 15, 2026

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

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

Published on: December 7, 2021

Ancestral population genomics using coalescence hidden Markov models and heuristic optimisation algorithms.

Jade Yu Cheng¹, Thomas Mailund¹

¹Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus, Denmark.

Computational Biology and Chemistry

|March 31, 2015

Summary

This study introduces a new framework for building complex coalescence hidden Markov models using full genome data. Heuristic optimization algorithms improve demographic inference accuracy for closely related species.

Keywords:

Coalescent hidden Markov models Demographic inference Genetic algorithm Numerical optimisation Particle swarm optimisation Sequential Markov coalescence

More Related Videos

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Related Experiment Videos

Last Updated: Apr 15, 2026

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

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

Published on: December 7, 2021

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Population genetics
Computational biology
Genomics

Background:

Full genome data availability enables advanced demographic inference.
Existing models struggle with complex demographic scenarios and require manual specification.
Sequential Markov coalescence and hidden Markov models (HMMs) are foundational.

Purpose of the Study:

To develop a flexible framework for constructing complex coalescence HMMs.
To implement heuristic optimization algorithms for parameter estimation.
To improve the accuracy of demographic inference from genomic data.

Main Methods:

Developed a framework for automated construction of coalescence HMMs for pairwise alignments.
Employed heuristic optimization algorithms for parameter estimation.
Compared performance against previous gradient-based approaches.

Main Results:

Successfully built more complex demographic models than previously possible.
Achieved more accurate parameter estimates using heuristic optimization.
Demonstrated a flexible and automated approach to model construction.

Conclusions:

The new framework facilitates the creation of sophisticated coalescence HMMs.
Heuristic optimization offers improved accuracy in parameter estimation for complex models.
This approach advances demographic inference capabilities using population genomic data.