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Related Concept Videos

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In the field of psychology, there are several ways to organize measurements of a trait, feature, or characteristic (i.e., variables). Qualitative data, such as ethnicity, can be tabulated into a frequency count to provide information about the proportion, as well as the variety of groups in a sample or population. On the other hand, researchers can perform a wider set of calculations on quantitative data. The mean, mode, and median, for instance, are central tendency measures to identify a...
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The standard deviation is the most common measure of variation. It is a value that tells us how far a data value is from the mean value in a dataset. Further, the standard deviation is always a positive value or zero.
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A Practical Guide to Phylogenetics for Nonexperts
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Phylogenetic rooting using minimal ancestor deviation.

Fernando Domingues Kümmel Tria1, Giddy Landan1, Tal Dagan1

  • 1Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel 24118, Germany.

Nature Ecology & Evolution
|February 2, 2018
PubMed
Summary
This summary is machine-generated.

Rooting phylogenetic trees is crucial for evolutionary insights. The new minimal ancestor deviation (MAD) method accurately determines evolutionary relationships, even with varying evolutionary rates, outperforming existing techniques.

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Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Bioinformatics

Background:

  • Determining ancestor-descendant relationships is fundamental to evolutionary theory.
  • Rooting phylogenetic trees is essential for inferring these evolutionary relationships.
  • Current rooting methods face limitations due to evolutionary rate heterogeneity and lack of auxiliary data.

Purpose of the Study:

  • To introduce a novel rooting approach, the minimal ancestor deviation (MAD) method.
  • To address limitations of existing methods in handling evolutionary rate heterogeneity (heterotachy).
  • To provide a robust and consistent method for rooting phylogenetic trees applicable to diverse datasets.

Main Methods:

  • The minimal ancestor deviation (MAD) method utilizes all pairwise topological and metric information from unrooted trees.
  • It accommodates evolutionary rate heterogeneity (heterotachy).
  • The method's performance was evaluated by analyzing phylogenetic trees of eukaryotes and prokaryotes.

Main Results:

  • MAD successfully recovered the known root of the eukaryotic tree.
  • The method provided evidence for the marine origin of cyanobacteria.
  • MAD demonstrated greater robustness and consistency compared to existing rooting methods.

Conclusions:

  • The minimal ancestor deviation (MAD) method offers a significant advancement in phylogenetic tree rooting.
  • It provides reliable root inference and measures of root inference quality.
  • MAD is a versatile tool applicable to any phylogenetic tree with branch lengths.