Mitochondrial phylogenomics reveals insights into taxonomy and evolution of Penaeoidea (Crustacea: Decapoda)

Abstract

The taxonomy and phylogeny of Penaeoidea have long been fraught with contro-versy. Here, we carried out the first mitochondrial phylogenomic analysis on all the penaeoid families and tribes, including nine newly sequenced and 14 published mi-togenomes, towards elucidating the phylogeny and evolutionary history of Penaeoidea. All these nine mitogenomes exhibit the pancrustacean ground pattern, except that Benthonectes filipes contains two additional clusters of tRNAAla, tRNAArg and tRNAAsn and an uncommon noncoding region. The resulted phylogenetic tree is generally well resolved with Benthesicymidae sister to Aristeidae, forming a clade with Solenoceridae. Contrary to traditional classification, this clade has a sister rela-tionship with the tribe Penaeini of the family Penaeidae. The family Sicyoniidae is deeply nested within the penaeid tribe Trachypenaeini which forms a sister clade with the remaining penaeid tribe, Parapenaeini. As the family Penaeidae is recovered to be polyphyletic, the three tribes in Penaeidae are all elevated to familial status. On the other hand, the family Sicyoniidae is retained to accommodate Trachypenaeini because they are now synonyms and the former name is more senior. This work is the first molecular analysis concurring with the latest findings in fossil assessments showing that Parapeaneini is the most primitive in Penaeoidae. Our results also il-lustrate a shallow‐water origin and an onshore–offshore evolutionary shift in penae-oid shrimps.