Phylogenomic analyses of Blattodea combining traditional methods, incremental tree-building, and quality-aware support.

Mol Phylogenet Evol

Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR7205, Muséum national d'Histoire naturelle (MNHN), CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50 Paris, France.

Published: November 2024

AI Article Synopsis

  • Despite advancements in genomics, assessing uncertainty in phylogenomic studies remains challenging, particularly in the phylogenetics of cockroaches and termites, where inconsistencies persist across different research.
  • A new phylogenetic analysis of Blattodea was conducted using three methods, including a novel "tiered phylogenetic inference," which integrates data quality into the analysis to better gauge the reliability of phylogenetic relationships.
  • This approach highlighted problematic areas with previously high support but low data quality, leading to clearer resolutions of several phylogenetic uncertainties, particularly regarding the relationships within Blaberidae and other families.

Article Abstract

Despite the many advances of the genomic era, there is a persistent problem in assessing the uncertainty of phylogenomic hypotheses. We see this in the recent history of phylogenetics for cockroaches and termites (Blattodea), where huge advances have been made, but there are still major inconsistencies between studies. To address this, we present a phylogenetic analysis of Blattodea that emphasizes identification and quantification of uncertainty. We analyze 1183 gene domains using three methods (multi-species coalescent inference, concatenation, and a supermatrix-supertree hybrid approach) and assess support for controversial relationships while considering data quality. The hybrid approach-here dubbed "tiered phylogenetic inference"-incorporates information about data quality into an incremental tree building framework. Leveraging this method, we are able to identify cases of low or misleading support that would not be possible otherwise, and explore them more thoroughly with follow-up tests. In particular, quality annotations pointed towards nodes with high bootstrap support that later turned out to have large ambiguities, sometimes resulting from low-quality data. We also clarify issues related to some recalcitrant nodes: Anaplectidae's placement lacks unbiased signal, Ectobiidae s.s. and Anaplectoideini need greater taxon sampling, the deepest relationships among most Blaberidae lack signal. As a result, several previous phylogenetic uncertainties are now closer to being resolved (e.g., African and Malagasy "Rhabdoblatta" spp. are the sister to all other Blaberidae, and Oxyhaloinae is sister to the remaining Blaberidae). Overall, we argue for more approaches to quantifying support that take data quality into account to uncover the nature of recalcitrant nodes.

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Source
http://dx.doi.org/10.1016/j.ympev.2024.108177DOI Listing

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