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

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...

Multiple Allele Traits

Multiple Allele Traits

The Concept of Multiple Allelism

What is a Species?

What is a Species?

Lethal Alleles

Lethal Alleles

Agouti: A Lethal Allele
Lucien Cuénot discovered lethal alleles in 1905 while studying the inheritance of coat color in mice. The agouti gene is responsible for the color of the coat in mice. This gene codes for an agouti-signaling protein, which is responsible for melanin distribution in mammals. The wild-type allele gives rise to gray-brown coat color in mice, while the mutant allele gives rise to yellow coat color. In addition to coat color, the agouti gene is associated with the yellow...

Keystone Species

Keystone Species

Measures of species biodiversity, such as richness (i.e., the number of species present) and evenness (i.e., their relative abundance), describe an ecological community’s structure. Many factors affect community structure, including abiotic factors (e.g., sunlight and nutrients), disturbances (e.g., fire or flood), species interactions (e.g., predation or competition), and chance events (e.g., foreign species invasion). Certain species—such as keystone species—also play a...

Formation of Species

Formation of Species

Speciation describes the formation of one or more new species from one or sometimes multiple original species. The resulting species are discrete from the parent species, and barriers to reproduction will typically exist. There are two primary mechanisms, speciation with and without geographic isolation—allopatric and sympatric speciation, respectively.

You might also read

Related Articles

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

Sort by

Same author

Phlag: scalable detection of genomics regions with unexplained phylogenetic heterogeneity.

Bioinformatics (Oxford, England)·2026

Same author

The Vertebrate Genomes Project Phase I: A global reference genome resource.

bioRxiv : the preprint server for biology·2026

Same author

DipSkmer: Reference-free population genomics with diploid genome skims.

bioRxiv : the preprint server for biology·2026

Same author

Phylogenomics beyond the 'bag-of-genes' model.

Trends in genetics : TIG·2026

Same author

ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances.

Genome biology·2026

Same author

Coalescent-based branch length estimation improves dating of species trees.

Systematic biology·2026

Search research articles

Related Experiment Video

Updated: Feb 3, 2026

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

Published on: December 1, 2014

Multi-allele species reconstruction using ASTRAL.

Maryam Rabiee¹, Erfan Sayyari², Siavash Mirarab²

¹Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States.

Molecular Phylogenetics and Evolution

|November 6, 2018

Summary

Sampling multiple individuals per species does not significantly improve species tree accuracy. Analyzing more genes is more effective than increasing individuals, even with high incomplete lineage sorting (ILS).

Keywords:

Gene trees ILS Multi-allele Multispecies coalescent Phylogenomics Species trees Summary method

More Related Videos

High-resolution Imaging and Analysis of Individual Astral Microtubule Dynamics in Budding Yeast

High-resolution Imaging and Analysis of Individual Astral Microtubule Dynamics in Budding Yeast

Published on: April 20, 2017

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Published on: September 20, 2020

Related Experiment Videos

Last Updated: Feb 3, 2026

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

Published on: December 1, 2014

High-resolution Imaging and Analysis of Individual Astral Microtubule Dynamics in Budding Yeast

High-resolution Imaging and Analysis of Individual Astral Microtubule Dynamics in Budding Yeast

Published on: April 20, 2017

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Published on: September 20, 2020

Area of Science:

Phylogenetics
Population Genetics
Genomics

Background:

Genome-wide phylogeny reconstruction is common, aiming to model gene tree discordance with species trees.
Incomplete lineage sorting (ILS) is a key driver of discordance, linking population genetics and phylogenetics.
Existing methods like ASTRAL typically require one sample per species.

Purpose of the Study:

To extend the ASTRAL species tree reconstruction method to handle multi-individual (multi-allele) datasets.
To introduce heuristic methods for optimizing the search space in multi-individual datasets.
To evaluate the accuracy and scalability of the multi-individual ASTRAL-III and compare it with NJst.

Main Methods:

Developed and implemented extensions to the ASTRAL quartet-based method for multi-individual data.
Introduced heuristic search space construction for multi-individual datasets.
Conducted extensive simulation studies to assess accuracy and scalability, comparing ASTRAL-III with NJst.

Main Results:

The quartet-based optimization naturally extends to multi-individual datasets.
No strong evidence suggests that using multiple individuals significantly enhances species tree accuracy.
Sampling more genes proved more beneficial than sampling more individuals, even in shallow trees with high ILS.

Conclusions:

The multi-individual version of ASTRAL is a viable extension for species tree reconstruction.
Prioritizing the analysis of more genes over more individuals is generally more effective for improving phylogenetic accuracy.
These findings are particularly relevant for studies with shallow evolutionary histories and high levels of incomplete lineage sorting.