Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies

Abstract

The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). In contrast, several molecular datasets have contradicted the Diplopoda–Pauropoda grouping (named Dignatha). Here we present the first transcriptomic data including a pauropod and both families of symphylans, allowing myriapod interrelationships to be inferred from phylogenomic data from representatives of all main lineages. Phylogenomic analyses consistently recovered Dignatha with strong support. Taxon removal experiments identified outgroup choice as a critical factor affecting myriapod interrelationships. Diversification of millipedes in the Ordovician and centipedes in the Silurian closely approximates fossil evidence whereas the deeper nodes of the myriapod tree date to various depths in the Cambrian-Early Ordovician, roughly coinciding with recent estimates of terrestrialisation in other arthropod lineages, including hexapods and arachnids. We provide a summary state-of-the-art Myriapoda Tree of Life at the ordinal level, the resolution of which has been improved by phylogenomics.

A deeper meaning for shallow‐level phylogenomic studies: nested anchored hybrid enrichment offers great promise for resolving the tiger moth tree of life (Lepidoptera: Erebidae: Arctiinae)

“…AHE also captures homologous DNA sequences shared at deep scales but aims to target relatively less-conserved regions using variable probes that represent the sequence diversity in the group under study (Lemmon et al, 2012). In the context of arthropod phylogenetics, these and other large genomic datasets have provided resolution across diverse lineages such as Myriapoda (Fernández et al, 2018), Insecta (Misof et al, 2014), Diptera (Young et al, 2016), Hymenoptera (Peters et al, 2017), Coleoptera (Shin et al, 2017;Zhang et al, 2018b;McKenna et al, 2019), Neuroptera (Winterton et al, 2018) and Arachnida (Hamilton et al, 2016), to name a few.…”

Differential gene expression during substrate probing in larvae of the Caribbean coral Porites astreoides

“…It is however worth noting that this is the first study to date that generated transcriptome data sets for individual coral larvae, adapting a protocol designed and optimized for microarthropods (Fernández, Edgecombe, & Giribet, ). Previous transcriptomic studies pooled coral larvae (e.g., Mansour et al, ; Meyer, Aglyamova, et al, ) to extract enough mRNA for RNA‐Seq library generation.…”

Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata

“…A dismissive attitude toward phylogenetic hypotheses based on morphology is therefore not warranted [ 68 , 149 , 155 , 158 , 159 ]. Many recent publications have employed phylogenomic data to resolve apparent conflicts between morphological and molecular data in favor of topologies originally supported by morphology alone, including the Strepsiptera problem [ 160 ], sponge paraphyly [ 161 ] and the relationships among the main clades of myriapods [ 162 ], copepods [ 163 ] and otophysan [ 95 ] and siluriform actinopterygians [ 164 ]. These examples illustrate that congruence between morphological and molecular evidence is still crucial for phylogenetics [ 149 ] and should be sought regardless of the amount of molecular data supporting any given hypothesis.…”