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

7.1K
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...
7.1K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

738
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
738
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

18.7K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
18.7K
DNA Microarrays02:34

DNA Microarrays

21.4K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
21.4K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

8.2K
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...
8.2K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.8K
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%...
18.8K

You might also read

Related Articles

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

Sort by
Same author

Genome assembly and annotation of a deep-diving pinniped, the northern elephant seal (Mirounga angustirostris).

The Journal of heredity·2025
Same author

Genetic, phenotypic, and environmental drivers of local adaptation and climate change-induced maladaptation in a migratory songbird.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Recent Adaptation in a Threatened Salmonid Revealed by Museum Genomics.

Molecular ecology·2025
Same author

A genome assembly for Lahontan Cutthroat Trout, Oncorhynchus clarkii henshawi.

The Journal of heredity·2025
Same author

Eradication efforts catalyze rapid evolution in an invasive predatory fish.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon.

Evolutionary applications·2025

Related Experiment Video

Updated: Feb 18, 2026

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

2.0K

Microhaplotypes provide increased power from short-read DNA sequences for relationship inference.

Diana S Baetscher1,2, Anthony J Clemento2,3, Thomas C Ng2,4

  • 1Department of Ocean Sciences, University of California, Santa Cruz, CA, USA.

Molecular Ecology Resources
|November 17, 2017
PubMed
Summary

This study introduces microhaplotypes from DNA sequencing, significantly improving the accuracy of identifying genetic relationships like full siblings and parent-offspring pairs in population genetics research.

Keywords:
high-throughput DNA sequencingmicrohaplotypeparentagepopulation geneticsrelationship inference

More Related Videos

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.8K
Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

39.9K

Related Experiment Videos

Last Updated: Feb 18, 2026

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

2.0K
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.8K
Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

39.9K

Area of Science:

  • Population genetics
  • Ecological genomics
  • Bioinformatics

Background:

  • High-throughput sequencing generates vast DNA data, presenting opportunities and challenges for ecological and population genetic studies.
  • Current methods often use single nucleotide polymorphisms (SNPs), overlooking valuable information in phased short-read DNA sequences.

Purpose of the Study:

  • To develop and validate a microhaplotype-based approach for enhanced relationship inference in population genetics.
  • To demonstrate the increased power and reduced false-positive rates of microhaplotypes compared to traditional SNP analysis.
  • To assess the implications of microhaplotypes for identifying various genetic relationships, including sibling and parent-offspring pairs.

Main Methods:

  • Targeted sequencing of regions with multiple SNPs in kelp rockfish (Sebastes atrovirens).
  • Calling microhaplotypes as alleles at each locus.
  • Comparing the performance of microhaplotype data versus bi-allelic SNP data for relationship inference.

Main Results:

  • Microhaplotype markers dramatically increase statistical power for relationship inference.
  • The microhaplotype approach reduces false-positive rates by several orders of magnitude for full-sibling and parent-offspring pair identification.
  • Analysis revealed that identifying half-sibling pairs is data-intensive and often underpowered in published studies.

Conclusions:

  • Phased short-read DNA sequence data and microhaplotype analysis offer a more efficient and powerful method for genetic relationship estimation.
  • This approach reduces the number of loci needed, lowering data collection costs and minimizing issues with physical linkage.
  • Advances in microhaplotype analysis will facilitate collaborative research and management of widespread species.