DOI: 10.5061/dryad.tmpg4f52d
title: Supporting data: Eocene origin of anemone carrying in polydectine crabs

description: 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.
description: 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. <br> 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 <em>Tunebia
 hatagumoana</em> and <em>L. edmosoni</em> 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, <em>L. leptochelis</em>, 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.
description: 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.