Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora)

Area of Science:

• Evolutionary Biology
• Genomics
• Phylogenetics

Background:

• Paleocene carnivores underwent rapid adaptive radiations, leading to speciation events that outpaced the fixation of phylogenetic markers.
• This rapid radiation resulted in incongruent genealogies and conflicting phylogenetic signals, complicating evolutionary studies.

Purpose of the Study:

• To explore conflicting phylogenetic zones in early arctoid radiation.
• To distinguish diagnostic from misleading phylogenetic signals using retroposed elements.
• To examine carnivore-related speciation events and resolve phylogenetic discordances.

Main Methods:

• Applied high-throughput computational strategies to screen carnivore genomes for randomly inserted retroposed elements.
• Utilized Long Interspersed Elements (LINEs) and Short Interspersed Elements (SINEs) as homoplasy-free phylogenetic markers.
• Employed a combined retrophylogenomic and in vitro wet lab approach for validation.

Main Results:

• Detected hundreds of carnivore-specific retroposed element insertions, confirming known splits and resolving conflicting species distributions.
• Identified homoplasy-free markers from LINEs with insertion-specific truncation points to differentiate informative signals.
• Results were independently confirmed by diagnostic SINEs, ruling out ancestral hybridization.

Conclusions:

• Conflicting phylogenetic patterns in Arctoidea are genomic remnants of ancestral incomplete lineage sorting.
• Retroposed elements provide reliable markers for resolving rapid, complex speciation events in evolutionary history.
• This approach successfully untangled phylogenetic discordances in the Arctoidea group.