Mining the mammalian genome for artiodactyl systematics

Area of Science:

• Molecular Phylogenetics
• Evolutionary Biology
• Comparative Genomics

Background:

• The evolutionary relationships within the order Artiodactyla (even-toed ungulates) have been challenging to resolve using traditional methods.
• Mitochondrial DNA (mtDNA) has been widely used, but can be prone to homoplasy and sensitive to sampling.
• Nuclear DNA markers offer a potentially more robust alternative for phylogenetic reconstruction.

Purpose of the Study:

• To reconstruct a robust phylogeny of the Artiodactyla using a comprehensive dataset of nuclear and mitochondrial DNA.
• To investigate the evolutionary history of key artiodactyl families and suborders.
• To compare the phylogenetic signal derived from nuclear DNA versus mtDNA.

Main Methods:

• Phylogenetic analysis of 7,806 nucleotide positions from one mitochondrial and eight nuclear DNA segments.
• Inclusion of 24 artiodactyl species, two cetacean species, and one outgroup (horse).
• Partition homogeneity tests and analyses of individual nuclear loci and indels to assess data congruence.

Main Results:

• Nuclear DNA analyses consistently supported a paraphyletic Artiodactyla, with Suiformes (pigs, peccaries) as the most basal Cetartiodactyla group.
• Mitochondrial DNA (cytochrome b) data exhibited high homoplasy and were unreliable for robust phylogenetic inference.
• Ruminantia was consistently monophyletic, with specific clades identified: Antilocaprinae as a unique lineage, Cervidae and Bovidae as sister taxa, and Giraffidae as more primitive.

Conclusions:

• Nuclear DNA provides a reliable framework for resolving artiodactyl phylogeny, challenging previous classifications based on mtDNA.
• The Artiodactyla, as traditionally defined, is paraphyletic, indicating a complex evolutionary history.
• Specific evolutionary relationships within Ruminantia and the basal position of Suiformes are clarified by nuclear DNA data.