A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans

Abstract

Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, ‘lobster’ and ‘crab’ groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic–Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.

The reniform body: An integrative lateral protocerebral neuropil complex of Eumalacostraca identified in Stomatopoda and Brachyura

“…As recognized by Hanström (), many other reptantians have highly modified centers that lack columnar lobes, which he nevertheless recognized as mushroom bodies but referred to as “hemiellipsoid bodies.” Those species also show evidence of reniform bodies (Strausfeld & Sayre, ). Observations of Varunidae and Ocypodidae (fiddler crabs), which belong to Brachyura, the evolutionarily youngest reptantian clade (Wolfe et al, ), verified they also possess centers corresponding to the stomatopod reniform body. In the varunid crab Neohelice granulata , this center is of particular interest because of evidence that it participates in learning and memory, expressed as long‐term habituation to noxious visual stimuli (Maza, Sztarker, Shkedy, Peszano, Locatelli, & Delorenzi, 2016).…”

Mushroom Body Homology and Divergence across Pancrustacea

“…Here we consider two species, both of which spend intertidal periods out of water; the shore crab Hemigrapsus nudus (Varunidae) and fiddler crab Uca (Minuca) minax (Ocypodidae). Fossil-calibrated molecular phylogenies indicate a mid to late Cretaceous origin for the Varunidae and Ocypodidae (Tsang et al, 2014;Wolfe et al, 2019).…”

“…Species considered here belong to eumalacostracan lineages whose divergence times are known from fossil-calibrated molecular data , and which are estimated to have originated some time between the mid-tolate Ordovician and the Carboniferous ( Figure 1A). The following descriptions include only a small number of the species belonging to lineages used for molecular phylogenomic reconstruction (see Schwentner et al, 2018;Wolfe et al, 2019). We have also referred to analyses that focus on mantis shrimps (Van der Wal et al, 2017), as well as decapods, including stenopods (cleaner shrimps), alpheids and carideans ("visored shrimps", "pistol shrimps": Anker et al, 2006;Anker and Baeza, 2012;Bracken et al, 2010;Davis et al, 2018), brachyurans ("true crabs": Tsang et al, 2014), thalassinids ("ghost shrimps": Tsang et al, 2008), anomurans including "hermit crabs" (Bracken-Grissom, 2014a;Chablais et al, 2011), and various clades that colloquially are referred to as lobsters (see Shen et al, 2013;Bracken-Grissom, 2014b).…”

“…Reptantia are estimated to have originated in the mid-late Devonian (Porter et al, 2005;Wolfe et al, 2019). They are a natural group comprising genera that all possess a novel satellite neuropil in the deutocerebrum, adjacent to the olfactory lobe (Sandeman et al, 1993).…”

“…The anomuran family Coenobitidae, to which the Caribbean land hermit crab belongs, is a recent group appearing approximately 35-40 mya (Bracken-Grissom et al, 2014a;Wolfe et al, 2019). Coenobita clypeatus and its cousin the coconut crab Birgus latro have attracted considerable attention regarding olfactory adaptations associated with terrestrialization (Stensmyr et al, 2005).…”