Molecular evolutionary processes and conflicting gene trees: the hominoid case

Area of Science:

• Molecular evolution
• Genomics
• Primate phylogeny

Background:

• Molecular evolutionary processes generate phylogenetic signal and homoplasy.
• DNA regions with tandem repeats are prone to homoplasy, potentially reducing phylogenetic reliability.
• Discrepancies exist in African hominoid phylogenies, with the involucrin gene presenting an exception to the human-chimpanzee clade.

Purpose of the Study:

• To investigate the reliability of DNA repeat regions in phylogenetic reconstruction.
• To reconcile conflicting molecular phylogenies within African hominoids.
• To understand the role of molecular evolutionary processes and polymorphisms in gene tree/species tree conflicts.

Main Methods:

• Analysis of DNA sequences, focusing on regions with tandem repeats.
• Comparative analysis of molecular datasets, including the involucrin gene and cytochrome oxidase subunit II (COII) gene.
• Evaluation of homoplasy and its impact on phylogenetic signal.

Main Results:

• Involucrin repeat regions present challenges for phylogenetic resolution due to alignment difficulties, insertions/deletions, and polymorphisms.
• Analysis of mitochondrial COII gene sequences, accounting for intraspecific variability, supports a human-chimpanzee clade.
• Humans and chimpanzees show the closest relationship, with gorillas exhibiting a similar degree of separation as in analyses using single individuals per species.

Conclusions:

• Phylogenetic conflicts in hominoid molecular data can be explained by molecular evolutionary processes and the sorting of ancient polymorphisms.
• Mitochondrial DNA variability supports the human-chimpanzee clade, highlighting the importance of considering intraspecific variation.
• A unified perspective integrating molecular evolution and population genetics can improve understanding of hominoid phylogenies.