The Y Chromosome is a Reliable Marker for Deep-Time Phylogenetic Inference

Area of Science:

• Evolutionary Biology
• Genomics
• Mammalian Phylogenetics

Background:

• The Y chromosome is an optimal phylogenetic marker due to reduced effective population size and barriers to gene flow, but its complex structure hinders cross-species alignment.
• Previous phylogenomic analyses have largely excluded the Y chromosome, limiting its use in understanding mammalian evolution.

Purpose of the Study:

• To develop a novel approach for identifying orthologous Y-linked sequences in placental mammals.
• To generate a robust Y-chromosome alignment for phylogenetic reconstruction.
• To investigate the utility of the Y chromosome as a phylogenetic marker across deep evolutionary timescales.

Main Methods:

• Developed a method to identify orthologous Y-linked sequences in placental mammals.
• Generated a 63-species Y-chromosome alignment using approximately 80 kilobases of predominantly non-coding sequence from X-degenerate genes.
• Performed phylogenetic reconstructions using Y-chromosomal data and compared them with genome-wide analyses.

Main Results:

• Successfully aligned Y-chromosomal sequences across species divergences exceeding 100 million years.
• Y-chromosome-based phylogenetic reconstructions strongly support controversial superordinal clades: Euarchonta, Scrotifera, Fereuungulata, and Zooamata.
• Non-coding X-degenerate gene sequences recapitulate phylogenies derived from autosomal and X-chromosomal data.
• Evidence of independent interchromosomal gene conversion between ZFX and ZFY genes in multiple lineages was found.

Conclusions:

• The Y chromosome can be reliably aligned and used for robust phylogenetic analyses across deep mammalian divergences.
• The Y chromosome confirms previously debated mammalian evolutionary groupings.
• Interchromosomal gene conversion between ZFX and ZFY may act as a compensatory mechanism against genetic decay of the essential ZFY gene.