Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

Abstract

Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.

Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera

“…A major component of modern phylogenomic analysis is the ability to remove, or ‘filter’, loci that appear to have undesirable qualities, such as missing data, base composition bias, or saturation (Borowiec et al . ; Fernández, Edgecombe & Giribet ; Meiklejohn et al . ).…”

“…It remains unclear how many loci are necessary to resolve the majority of phylogenetic relationships, but we believe that having a greater number of loci to work with is beneficial. A major component of modern phylogenomic analysis is the ability to remove, or 'filter', loci that appear to have undesirable qualities, such as missing data, base composition bias, or saturation (Borowiec et al 2015;Fern andez, Edgecombe & Giribet 2016;Meiklejohn et al 2016). Consequently, having more loci gives researchers greater flexibility to remove potentially problematic loci, resulting in more robust analyses and results.…”

Genomics and the animal tree of life: conflicts and future prospects

“…Now that data quantity is not a limiting factor any longer, data quality is playing an increasing role in phylogenomic studies, designing data sets to resolve specific nodes (e.g. Dell'Ampio et al 2014;Fern andez et al 2014Fern andez et al , 2016Sharma et al 2014;Andrade et al 2015). Similarly designed data sets should help us to better understand the most difficult nodes of the animal tree, specifically at its very root.…”

Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida)

“…Comparative morphological, molecular and higher-level systematic evidence has largely confirmed the monophyly of myriapods (Boudreaux 1979; Ax 1999; Bitsch and Bitsch 2004; Gai et al 2006; Bäcker et al 2008; Regier et al 2008, 2010; Rehm et al 2014; Fernández et al 2016), even though this was once a controversial topic (Pocock 1893; Snodgrass 1952; Dohle 1980). The phylogeny of the millipedes is still an open topic regarding their position within the Myriapoda and earliest splits inside the diplopod lineage (Edgecombe 2011; Fernández et al 2016). …”