---
title: "Phylogenomics: Gene Trees, Species Trees and Why They Disagree"
description: "Different genes give different trees for the same set of species, through incomplete lineage sorting, introgression, duplication and plain estimation error. This stop separates those causes and uses m"
canonical: https://lightmysky.com/learn/science/phylogenomics-gene-trees-species-trees-and-why-they-disagree-mt_rg7feIg1D4
source: https://lightmysky.com/learn/science/phylogenomics-gene-trees-species-trees-and-why-they-disagree-mt_rg7feIg1D4.md
retrieved: 2026-09-12
---

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# Phylogenomics: Gene Trees, Species Trees and Why They Disagree

Different genes give different trees for the same set of species, through incomplete lineage sorting, introgression, duplication and plain estimation error. This stop separates those causes and uses methods that expect the conflict instead of hiding it.

Subject: Science · Area: Genetics & Evolution · Ages 22 to 24
Page: https://lightmysky.com/learn/science/phylogenomics-gene-trees-species-trees-and-why-they-disagree-mt_rg7feIg1D4

## Ready when they can

- Distinguish incomplete lineage sorting from introgression using tree topology counts and site patterns
- Explain when concatenating genes is misleading and what a coalescent summary method does instead
- Read a set of gene trees and locate the nodes where the conflict is real rather than noise

## Lesson: Why genes disagree about the species tree

You keep the species tree apart from gene trees in your head. The species tree records how populations split. Each gene has its own history, and it can differ for purely biological reasons.

You learn the classic cause first. When ancestral populations are large and splits come quickly, gene variants fail to sort neatly into the descendant species. This incomplete lineage sorting clusters at short internal branches, and you model it rather than average it away.

**Example.** You string all your genes into one giant alignment and get full support for one tree. But the genes genuinely disagree, so concatenation has converged on the wrong answer with full confidence. You switch to a coalescent summary method: you infer each gene tree, then find the species tree most consistent with the distribution.

**Tip.** You separate the two causes with topology counts plus site patterns. Sorting spreads discordance symmetrically, while gene flow enriches exactly the topology grouping the exchanging partners, with linked sites sharing the pattern. Estimation error shrinks with longer sequences, but true conflict persists with structure.

**Recap.** You expect gene conflict at short branches, you distrust concatenation under discordance, and you separate sorting from gene flow with counts plus site patterns.

## Practice

8 questions on this page, each with its working shown.

## Needs first

- [Bayesian Phylogenetics: Priors, Sampling and Judging Convergence](https://lightmysky.com/learn/science/bayesian-phylogenetics-priors-sampling-and-judging-convergence-mt_7jWhYh1n5X)
- [Genetic Drift and Effective Population Size](https://lightmysky.com/learn/science/genetic-drift-and-effective-population-size-mt_lbB1GbKv_t)
- [Using Trees: Ancestral States, Dates and Comparative Tests](https://lightmysky.com/learn/science/using-trees-ancestral-states-dates-and-comparative-tests-mt_lEYWID9Ffs)