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Review
.2023 Aug 3;40(8):msad175.
doi: 10.1093/molbev/msad175.

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

Affiliations
Review

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

James P Bernot et al. Mol Biol Evol..

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.

Keywords: Crustacea; Malacostraca; Pancrustacea; copepod; evolution; phylogeny.

Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution 2023.

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Figures

<sc>Fig.</sc> 1.
Fig. 1.
Morphological diversity of select pancrustaceans: (A) buoy barnacle (Cirripedia), (B)Daphnia sp. (Branchiopoda), (C) skeleton shrimp (Amphipoda), (D)Argulus sp. (Branchiura), (E) Japanese spider crab (Decapoda), (F) parasitic copepod (Copepoda), (G)Lasionectes entrichoma (Remipedia), (H) seed shrimp (Ostracoda), (I) comma shrimp (Cumacea), (J) sweat bee (Hexapoda), (K) mantis shrimp (Stomatopoda), and (L) giant isopod (Isopoda). Image credits: (A) David Fenwick, (B) Marek Miś, (C) David Fenwick, (D) Andrei Savitsky, (E) Michael Wolfe and Hans Hillewaert, (F) Geoff Boxshall, (G) Jørgen Olesen, (H) Anna Syme, (I) Hans Hillewaert, (J) USGS Bee Inventory and Monitoring Lab, (K) Roy L. Caldwell, and (L) Chan T.Y. and Lin C.W.
<sc>Fig.</sc> 2.
Fig. 2.
(A) Tree resulting from ML analysis of the Data set 2 AA matrix using LG + C60 + F + G model. Species marked with an asterisk are additional taxa included in Data set 2 relative to Data set 1. (B) Recent phylogenomic hypotheses of pancrustacean relationships.
<sc>Fig.</sc> 3.
Fig. 3.
Topological comparisons. Data set 2: (A) MDS of topological tree space of phylogenetic analyses in this study using the Kendall and Colijn (2016) method for defining summary trees, (B) C60 + LG + F + G, (C) CAT-GTR majority-rule consensus, (D) CAT-GTR majority-rule consensus of Dayhoff6 matrix, and (E) ASTRAL resulting from analysis of gene tree nodes with <30% BS collapsed and nodes <0.5 PP collapsed. Data set 1: (F) C60 + LG + F + G, (G) CAT-GTR majority-rule consensus, and (H) CAT-GTR majority-rule consensus of Dayhoff6 matrix with nodes <0.5 PP collapsed (nodes differed between chains after >80,000 generations).
<sc>Fig.</sc> 4.
Fig. 4.
Fossil calibrated divergence time estimates for Pancrustacea, based on an MCMCtree analysis of the topology depicted in figure 2A calibrated with 13 vetted fossils. The fossil calibrated nodes have their posterior age distributions highlighted in light pink.
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