Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

Abstract

The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata). In addition to Hexapoda, Pancrustacea includes three major extant lineages of 'crustaceans', each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that 'crustaceans' are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.

Regressive evolution of the arthropod tritocerebral segment linked to functional divergence of the Hox genelabial

“…Myriapods also lack limbs on the tritocerebral segment [27,28]. This limb loss has previously been regarded as homologous in myriapods and insects and served as the key character for uniting the two groups in the taxon Antennata [28], but recent molecular phylogenies do not support the Antennata taxon and place the myriapods at the base of all mandibulate arthropods [29]. Accordingly, limb loss on the tritocerebral segment in insects and in myriapods has evolved by convergence.…”

“…Accordingly, limb loss on the tritocerebral segment in insects and in myriapods has evolved by convergence. Another intriguing case is the Pycnogonida (sea spiders), an enigmatic arthropod group usually considered as relatives of spiders and other chelicerates [29,30]. Some species of Pycnogonida lack the pedipalp limbs, while other species have them fully formed [31].…”

Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

“…For example, large-scale sequencing projects have been undertaken for many important clades, in which hundreds of loci are sequenced (e.g. Dunn et al, 2008;Regier et al, 2010;Kocot et al, 2011;Chiari et al, 2012;Struck et al, 2011;Jarvis et al, 2014;Weigert et al, 2014). Yet, at the same time, most species in many clades may still have data for no more than a few genes each (see below).…”

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

“…Evolutionarily, Collembola are closely related to insects, and together with Diplura these comprise the Hexapoda [48]. Collembolan fossils of Rhyniella praecursor from the Devonian (ca 400 million years ago (Mya)) are among the oldest known records of terrestrial arthropods.…”