Evaluating topological conflict in centipede phylogeny using transcriptomic data sets.

Area of Science:

• * Zoology
• * Evolutionary Biology
• * Genomics

Background:

• * Centipede (Chilopoda) phylogeny has been primarily based on morphological data.
• * Previous studies showed congruence between morphology and limited gene data, except for the placement of Craterostigmomorpha.
• * This discrepancy highlights potential limitations in traditional phylogenetic methods.

Purpose of the Study:

• * To resolve the phylogenetic incongruence concerning the placement of Craterostigmomorpha.
• * To utilize novel transcriptomic data for a comprehensive centipede phylogeny.
• * To investigate gene-tree incongruence as a factor in phylogenetic uncertainty.

Main Methods:

• * Generation of novel transcriptomic data for all five extant centipede orders.
• * Phylogenetic analyses using Maximum Likelihood and Bayesian mixture models.
• * Analysis of a large dataset (1,934 orthologs) and a subset of high-quality data (389 orthologs).

Main Results:

• * Strong support for a sister-group relationship between Craterostigmomorpha and the newly defined Amalpighiata (all other pleurostigmophoran centipedes).
• * The proposed Amalpighiata hypothesis demonstrated minimal gene-tree incongruence and robustness to data biases.
• * Evidence suggests convergent evolution in morphological and behavioral traits previously used for classification.

Conclusions:

• * The study redefines centipede evolutionary history by integrating transcriptomic data.
• * The findings necessitate a re-evaluation of morphological characters in centipede phylogenetics.
• * The new phylogeny aligns with existing fossil records, providing a more robust evolutionary framework.