Mitochondrial data are not suitable for resolving placental mammal phylogeny

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Mitochondrial DNA (mtDNA) is a valuable marker for reconstructing species phylogenies due to low recombination rates and extensive characterization in vertebrates.
• Phylogenetic placement of mammal species has been challenging due to limited fully sequenced genomes and insufficient taxon sampling within major groups.
• Utilizing large-scale mammalian mtDNA sequences could potentially overcome taxon-sampling deficits in phylogenetic studies.

Purpose of the Study:

• To evaluate the efficacy of mitochondrial DNA as a phylogenetic marker for resolving mammal species relationships.
• To investigate whether filtered mtDNA datasets can provide consistent and well-resolved phylogenies for mammals.

Main Methods:

• Mammalian mtDNA datasets were curated by sparse sampling across the phylogenetic tree and focusing on genes with high taxon coverage.
• Site-specific evolutionary rates were categorized independently of phylogeny, and fast-evolving sites were removed.
• Sampling was restricted to shallow divergence times to minimize phylogenetic conflict.

Main Results:

• Phylogenetic topologies derived from filtered mtDNA data were inconsistent with prior studies and showed discordance among different genes.
• Analysis of individual mitochondrial genes and a combined supermatrix yielded poor resolution of the mammalian species phylogeny.
• The applied filtering methods did not improve phylogenetic accuracy or resolution.

Conclusions:

• Mitochondrial DNA data, even after rigorous filtering, demonstrates significant limitations for resolving both deep and shallow divergences in mammalian phylogenetics.
• The study underscores the challenges in establishing robust mammal phylogenies using current mtDNA datasets and methodologies.
• Alternative or complementary genomic approaches may be necessary for accurate reconstruction of mammalian evolutionary history.