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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...

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Updated: Feb 23, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Objective choice of phylogeographic models.

Bryan C Carstens¹, Ariadna E Morales¹, Nathan D Jackson²

¹Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210-1293, United States.

Molecular Phylogenetics and Evolution

|September 10, 2017

Summary

Objective phylogeographic model selection using PHRAPL revealed that gene flow and population divergence are key evolutionary processes. This approach complements researcher intuition for analyzing genetic diversity.

Keywords:

Coalescent theory Gene flow Model selection Phylogeography

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Area of Science:

Evolutionary biology
Genetics
Ecology

Background:

Phylogeography investigates evolutionary processes driving organismal and genetic diversity.
Evaluating explicit hypotheses (models) with genetic data is crucial for understanding these processes.
Model-based tools for estimating phylogeographic parameters have advanced, but comparing complex models remains challenging.

Purpose of the Study:

To assess the adequacy of intuitive model selection in phylogeography.
To compare objective model selection with researcher intuition using empirical datasets.
To identify the most explanatory models for phylogeographic data.

Main Methods:

Reanalyzed 20 empirical phylogeographic datasets.
Utilized PHRAPL, an objective tool for phylogeographic model selection.
Compared model performance based on gene flow and population divergence parameters.

Main Results:

Objective model selection identified models incorporating both gene flow and population divergence as optimal for most datasets.
Species tree methods, which exclude gene flow, were found to be overly simplistic for many phylogeographic systems.
PHRAPL demonstrated the utility of objective approaches in phylogeographic analysis.

Conclusions:

Objective phylogeographic model selection provides a quantitative complement to researcher intuition.
Accurate phylogeographic inference requires models that account for gene flow and population divergence.
Advanced tools like PHRAPL enhance the rigor of evolutionary process discovery.