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Updated: Jun 21, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
An updated phylogeny and adaptive evolution within Amaranthaceae s.l. inferred from multiple phylogenomic datasets
Hao Xu1,2, Yuqin Guo3, Mingze Xia4
1Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China.
The Amaranthaceae family
Area of Science:
- Plant Science
- Evolutionary Biology
- Genomics
Background:
- Amaranthaceae s.l. is a diverse plant family with complex evolutionary relationships.
- Previous studies suggest Amaranthaceae s.s. and Chenopodiaceae form a monophyletic group, but internal relationships remain unclear.
Purpose of the Study:
- To resolve phylogenetic relationships within Amaranthaceae s.l.
- To investigate evolutionary patterns and drivers within the family.
Main Methods:
- Assembly of complete plastomes and full-length ITS sequences from 21 Amaranthaceae s.l. individuals.
- Comparative analysis of plastome structure, sequence alignment, and adaptive evolution.
- Phylogenetic tree construction and partitioned evolutionary analysis.
Main Results:
- Identified a 5200 bp reverse complementary region in Atriplex and Chenopodium.
- Detected significant positive selection in eight genes, driving Amaranthaceae s.l. evolution.
- Found two-thirds of species lack the ycf15 gene, suggesting adaptation to habitats.
- Phylogenetic analysis revealed paraphyletic genera (Chenopodium, Halogeton, Subtr. Salsolinae).
Conclusions:
- Results support Amaranthaceae s.l. clustering with monophyletic Chenopodiaceae and Amaranthaceae s.s.
- Cytonuclear conflict, habitat-driven gene selection, and incomplete lineage sorting explain phylogenetic inconsistencies.
- Rapid differentiation and adaptation during the last glacial period influenced species evolution.
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