The effect of model choice on phylogenetic inference using mitochondrial sequence data: lessons from the scorpions

Area of Science:

• Arthropod genomics
• Molecular evolution
• Systematic biology

Background:

• Chelicerates, a diverse arthropod group, have complex evolutionary relationships.
• Previous phylogenetic studies using mitochondrial genomes have yielded contentious results.
• Mitochondrial genome strand-bias can potentially compromise phylogenetic reconstruction.

Purpose of the Study:

• To investigate the phylogenetic position of scorpions within Chelicerata using mitochondrial genome data.
• To assess the impact of model mis-specification and strand-bias on phylogenetic inference.
• To refine understanding of interordinal relationships within Chelicerata.

Main Methods:

• Sequencing and analysis of the mitochondrial genome of the scorpion Mesobuthus gibbosus.
• Phylogenetic analyses using mitochondrial gene order and sequence data.
• Comparison of phylogenies under different evolutionary models, including the Neutral Transitions Excluded (NTE) model.

Main Results:

• The placement of scorpions at the base of Chelicerata was identified as an artifact of model mis-specification.
• Scorpions are strongly supported as basal arachnids.
• An expanded dataset supported interordinal relationships, such as ticks and mites (Acari) and spiders, whip spiders, and whip scorpions (Araneae+Pedipalpi).

Conclusions:

• Mitochondrial sequence data can be subject to systematic bias, leading to misleading evolutionary inferences.
• Careful methodological approaches are crucial when inferring chelicerate phylogenies from mitochondrial data.
• This study refines the understanding of chelicerate evolutionary history and relationships.