Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling

Abstract

The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies.

Phylogenetic and transcriptomic characterization of insulin and growth factor receptor tyrosine kinases in crustaceans

“…physiological processes is conserved across the Metazoa. RTK subclades often contained diverse pancrustacean taxa, and their topologies mirrored pancrustacean evolutionary history (74). This suggests that ancient duplication events gave rise to the diversity of RTKs observed today (31).…”

“…Interestingly, while the other receptors distributed into a number of subclades, EGFR was highly conserved across crustacean taxa, suggesting that its role in physiological processes is conserved across the Metazoa. RTK subclades often contained diverse pancrustacean taxa, and their topologies mirrored pancrustacean evolutionary history ( 74 ). This suggests that ancient duplication events gave rise to the diversity of RTKs observed today ( 31 ).…”

Discordance between phylogenomic datasets in aphids: who is telling the truth?

“…(2017) though we employed very similar analytical tools but on an extended taxon sampling. This suggests that phylogenetic resolution using mitogenome data is very sensitive to taxon sampling which usually indicates difficulties in estimating substitution models (Bernot et al . 2023).…”

“…In addition, our tree is very different from the one obtained by Chen et al (2017) though we employed very similar analytical tools but on an extended taxon sampling. This suggests that phylogenetic resolution using mitogenome data is very sensitive to taxon sampling which usually indicates difficulties in estimating substitution models (Bernot et al 2023). The nuclear DNA data does not yield a more stable hypothesis.…”

Incomplete lineage sorting and long-branch attraction confound phylogenomic inference of Pancrustacea

“…With the advent of DNA sequencing technology, molecular phylogenetics has dramatically improved the resolution of the relationship between and within Hexapoda + Crustacea. The nesting of Hexapoda within Crustacea is commonly revealed by recent molecular and morphological analyses (Meusemann et al, 2010;Andrew, 2011;Rota-Stabelli et al, 2011;Borner et al, 2014;Dell'Ampio et al, 2014;Lozano-Fernandez et al, 2016;Bernot et al, 2023). Within Pancrustacea, most phylogenomic and morphological analyses supported three major lineages: Oligostraca as the earliest diverging clade (including classes Branchiura, Mystacocarida, Ostracoda and Pentastomida), and two sister clades (Regier et al, 2010;Von Reumont et al, 2012;Oakley et al, 2013;Schwentner et al, 2017;Schwentner et al, 2018;Lozano-Fernandez et al, 2019), namely Allotriocarida (including classes Branchiopoda, Cephalocarida, Remipedia, and subphylum Hexapoda) (Lee et al, 2013;Lozano-Fernandez et al, 2016;Schwentner et al, 2017) and Multicrustacea (including classes Malacostraca, Copepoda and Thecostraca) (Meusemann et al, 2010;Andrew, 2011;Lee et al, 2013;Oakley et al, 2013;Eyun, 2017;Schwentner et al, 2017).…”