Dendrobranchiata and several infraorders of Pleocyemata (Caridea, Achelata, Astacidea, Anomura, and Brachyura) are the focal taxa.
Decapods are the most recognizable of all crustaceans [46], [47], and include the "true" crabs (Brachyura), hermit crabs and their relatives (Anomura), shrimps (Dendrobranchiata, Caridea and Stenopodidea), and lobsters (Astacidae, Thalassinidea), among other lesser known groups [47].
They consist of representatives from infraorders Brachyura (5), Axiidea (4), Gebiidea (3), Caridea (4), and suborder Dendrobranchiata (2).
Additionally, relationships within the remaining eucarids were altered, with the subtree of Procaridea to Dendrobranchiata re-rooted on Dendrobranchiata (such that Procaridea + Caridea formed the most highly internested clade).
Inside the type I clade, the clade of Dendrobranchiata (peneid shrimps) CHHs encoded by three-exon genes is at the base of the other decapod CHHs, encoded by four-exon genes, found both in Dendrobranchiata and Pleocyemata (the remaining decapods).
Our study includes representatives from 19 of the 20 anomuran families and 18 outgroup taxa sampled across Decapoda (Dendrobranchiata, Caridea, Axiidea, Gebiidea, Brachyura) (Table 1).
Although the first pleopods form a petasma in males (as is autapomorphic for Dendrobranchiata) no differences concerning the studied structures were found in the two sexes.
However, in the amino acid tree, the Caridea shows a sister position of the Dendrobranchiata, which also remains modestly statistically supported (MP/ML/BPP = 61/70/0.80).
The clustering of Macrobrachium with the two Dendrobranchiata makes the Pleocyemata paraphyletic (all Decapoda included here except for Marsupenaeus and Penaeus).
Because of the weak support, in the ML phylogeny, at the node indicating the duplication which led to the two paralogous CHH genes found in Dendrobranchiata (with three or four exons), an alternative topology was considered for pancrustacean CHH family genes, where the CHH gene duplication would have occurred only in the Dendrobranchiata phylum.
The nucleotide and amino acid trees are nearly the same except for the position of the Caridea clade (Halocaridina rubra + Macrobrachium rosenbergii) and the inner structure of the Dendrobranchiata clade.
