Here we study the evolutionary history of an elusive marine invertebrate and the origin of their specialized behavior. The crabs in the sub-family Polydectinae (family Xanthidae) have adapted to a defense behavior in which living invertebrates are used as protection from predators. All polydectine species carry a living invertebrate, usually a sea anemone or nudibranch, in each claw, that is positioned in front of the body and waved to scare off attackers. In an attempt to trace the origin of this behavior, we sequenced the complete mitochondrial genome of 19 crabs using museum samples. The complete mitochondrial genomes were included in a larger data set with previously published sequences and analyzed using maximum likelihood and Bayesian phylogenetic reconstruction. The divergence times of the polydectine crab radiation were estimated using the mitochondrial data set and several fossil calibration points. Our results show that the anemone-carrying polydectine crabs emerged in the late Eocene and consist of at least three deep evolutionary lineages. All three lineages share the unique behavior suggesting that it emerged in the ancestor to Polydectinae nearly 40 million years ago and have persisted in all living species.

This data set consists of 3 sequence alignments and 19 mitochondrial genome annotations.

Data set 1: complete mt genome alignment

The protein-coding genes were extracted from the 19 complete mt genomes. In addition, the protein-coding genes were extracted from 29 published mt genomes. The 13 protein-coding genes were aligned with MAFFT on the amino acid level using default settings (Katoh et al. 2019) and manually inspected. The mt genes were concatenated in MEGA11 (Tamura et al 2021) leading to a final alignment of 11,184 bp/3,728 aa.

Data set 2: partial CO1 alignment

Partial CO1, 12S and 16S sequences from GenBank of Lybia, Polydectus and the outgroup Cymo (Lai et al 2011) were aligned using MUSCLE implemented in Aliview (Larsson 2014). The newly generated species were included in the alignment and this was trimmed to keep the sequences of equal length.

The first alignment of partial CO1 sequences (599 bp) includes 21 sequences, including Tunebia hatagumoana and L. edmosoni and four outgroups.

Data set 3: partial CO1, 12S, 16S  alignment

The concatenated alignment of partial CO1, 12S and 16S sequences (18 sequences, 1,471 bp) was generated to include one additional polydectine, species, L. leptochelis, for which no CO1 sequence is available. 

Mt genome annotations

The MITOS2 (http://mitos2.bioinf.uni-leipzig.de/index.py) pipeline was used for annotation using standard settings [Refseq 63 Metazoa] and the invertebrate genetic code [code 5] (Donath et al 2019). All annotations were manually checked using comparative alignments and corrected when needed in Geneious Prime 2022.1.1 (https://www.geneious.com/). Each sequence was exported in GenBank format for easy downstream handling.

The fasta alignments can be opened using alignment viewers such as AliView (https://ormbunkar.se/aliview/) or MEGA11 (https://www.megasoftware.net/). The alignments can also be viewed in a simple text editor such as atom or text-wrangler.

The GenBank files can be opened in Geneious (https://www.geneious.com/) or in phylosuite (https://dongzhang0725.github.io/).  The files can also be viewed in a simple text editor such as atom or text-wrangler.