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Related Concept Videos

Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...
Evolutionary Relationships through Genome Comparisons02:54

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...
Phylogenetic Trees03:21

Phylogenetic Trees

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

Phylogenetic Trees

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
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Gene Evolution - Fast or Slow?

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.
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Related Experiment Video

Updated: Jul 2, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Principal Components Analysis Fails to Recover Phylogenetic Structure in Hominins.

Levi Y Raskin1, Maja Šešelj2, Bárbara D Bitarello3

  • 1Department of Integrative Biology, University of California, Berkeley, California, USA.

American Journal of Biological Anthropology
|July 1, 2026
PubMed
Summary

Principal components analysis (PCA) of hominin fossils is unreliable for inferring evolutionary relationships. Proximity in principal components (PC) space does not accurately reflect phylogenetic affinity, necessitating reevaluation of past interpretations.

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Area of Science:

  • Paleoanthropology
  • Evolutionary Biology
  • Biometry

Background:

  • Geometric morphometrics and principal components analysis (PCA) are widely used by paleoanthropologists to study hominin fossil shape variation.
  • Proximity in principal components (PC) space is often interpreted as indicating phylogenetic relationships, but this assumption lacks direct evaluation in hominins.

Purpose of the Study:

  • To evaluate the reliability of using principal components analysis (PCA) for inferring phylogenetic relationships from hominin fossil shape data.
  • To determine if proximity in PC space accurately reflects evolutionary affinity in hominins.

Main Methods:

  • Simulated 2D and 3D geometric morphometric and traditional morphometric datasets on inferred hominin phylogenies.
  • Performed PCA on simulated datasets and inferred evolutionary trees using neighbor-joining from PC scores.
  • Quantified differences between PCA-inferred trees and true phylogenies using subtree pruning and regrafting and Robinson-Foulds distances.

Main Results:

  • PCA trees inferred from traditional morphometric data matched the true phylogeny in only 0.11% (using 2 PCs) to 2.9% (using all PCs) of cases.
  • No PCA tree inferred from any of the 2.4 million simulated shape datasets matched the true phylogeny, irrespective of the number of axes used.

Conclusions:

  • Phylogenetic interpretations of hominin fossils based on proximity in PC space are fundamentally flawed and prone to error.
  • Previous systematic arguments relying on PCA in hominin studies should be critically re-examined using phylogenetically sound methods.