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Related Experiment Video

Updated: Oct 5, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Placing Ancient DNA Sequences into Reference Phylogenies.

Rui Martiniano^1,2, Bianca De Sanctis^1,3, Pille Hallast^4,5

¹Department of Genetics, University of Cambridge, Cambridge, United Kingdom.

Molecular Biology and Evolution

|January 27, 2022

Summary

This summary is machine-generated.

We developed pathPhynder, a new workflow for analyzing ancient DNA (aDNA). It improves phylogenetic placement and haplogroup assignment for ancient samples, even with low-quality data.

Keywords:

Y chromosome haplogroups ancient DNA phylogenetic placement

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Published on: August 16, 2017

Area of Science:

Ancient DNA analysis
Population genetics
Phylogenetics

Background:

Analyzing ancient DNA (aDNA) alongside modern phylogenies is challenging due to low sequence coverage and DNA damage.
Existing methods can lead to inaccurate or overly cautious phylogenetic assignments.
Accurate placement of ancient samples is crucial for understanding population history.

Purpose of the Study:

To introduce pathPhynder, an efficient likelihood-based workflow for improved ancient DNA phylogenetic analysis.
To enhance the accuracy of haplogroup assignment for ancient samples, particularly those with low sequence coverage.
To provide insights into ancient human migrations and population relationships using aDNA data.

Main Methods:

Developed pathPhynder, a novel workflow utilizing all polymorphic sites in target sequences.
Implemented a likelihood-based approach to evaluate ancestral and derived alleles on phylogenetic branches.
Compiled a comprehensive Y chromosome variation dataset (120,908 markers from 2,014 samples) for improved haplogroup assignment.

Main Results:

pathPhynder demonstrated improved Y chromosome haplogroup assignments for published aDNA sequences.
The workflow effectively places ancient samples in phylogenies, providing likely assignments and supporting evidence.
Application to African aDNA revealed new insights into ancient migrations and population dynamics.

Conclusions:

pathPhynder offers an efficient and accurate method for analyzing ancient DNA phylogenetics and haplogroup assignment.
The workflow significantly enhances the utility of low-coverage aDNA data for population genetics studies.
This approach provides valuable tools for exploring ancient human history and population connections.