DOI: 10.5061/dryad.k6djh9w50
title: Flexibility in Red Sea Tridacna maxima-Symbiodiniaceae associations supports environmental niche adaptation datasets

description: Giant clams (Tridacninae) are important members of Indo-Pacific coral
 reefs and among the few bivalve groups that live in a symbiosis with
 unicellular algae (Symbiodiniaceae). Despite the importance of these
 endosymbiotic dinoflagellates for clam ecology, the diversity and
 specificity of these associations remains relatively poorly studied,
 especially in the Red Sea. Here, we used the internal transcribed spacer 2
 (ITS2) rDNA gene region to investigate Symbiodiniaceae communities
 associated with Red Sea Tridacna maxima clams. We sampled five sites
 spanning 1,300 km (10° of latitude, from the Gulf of Aqaba, 29°N, to the
 Farasan banks, 18°N) along the Red Sea’s North-South environmental
 gradients. We detected a diverse and structured assembly of
 host-associated algae with communities demonstrating region- and
 site-specificity. Specimens from the Gulf of Aqaba harbored three genera
 of Symbiodiniaceae, i.e. Cladocopium, Durusdinium, and Symbiodinium,
 whilst at all other sites clams associated exclusively with algae from the
 Symbiodinium genus. Of these exclusively Symbiodinium-associating sites,
 the more northern (27° and 22°) and more southern sites (20° and 18°)
 formed two separate groupings despite site-specific algal genotypes being
 resolved at each site. These groupings were congruent with the genetic
 break seen across multiple marine taxa in the Red Sea at approximately
 19°, and along with our documented site specificity of algal communities,
 contrasted the panmictic distribution of the T. maxima host. As
 such, our findings indicate a flexibility in T. maxima-Symbiodiniaceae
 associations that may explain its relatively high environmental plasticity
 and offers a mechanism for environmental niche adaptation.
description: The SymPortal files were
 output directly from the remote instance of SymPortal. The SymPortal Files
 are: clam_profiles_absolute.txt clam_seqeunces_absolute.txt braycurtis_sample_distances_a_sqrt.dist clam_sequences.fasta The pappas_weber_alignment.fasta was created as such: Reanalysis of ITS1-5.8S-ITS2 haplotypes from previous characterizations          <br> Two previous clam-Symbiodiniaceae characterizations exist from the Red Sea (i.e. Weber 2009 and Pappas et al. 2017). These studies characterized the dominant Symbiodiniaceae genotypes by analyzing the full ITS region (ITS1-5.8S-ITS2) of the rRNA array resolved via Sanger sequencing. To assess for similarity in sampled haplotypes between these studies, we collated all sequences of Red Sea origin from them, computed a multiple sequences alignment using MAFFT (Katoh and Standley 2013), cropped at the 5’ and 3’ end of the alignment so that, with the exception of three short sequences that were removed from the alignment, all sequences were represented across the full alignment length. For reference, the A1 ITS2 sequence, as defined in the SymPortal remote database (symportal.org) was included in the alignment (independent of any cropping). SIMPER analysis To further investigate the sequences driving structure in the Bray-Curtis-derived distances we conducted a SIMPER analysis (Clarke 1993) on the post-MED <i>Symbiodinium</i> sequences with site as the grouping factor. Conducted in Python, we used ecopy’s simper function.
description: This data submission
 includes the SymPortal outputs and multiple sequence alignments that were
 generated and used as part of the associated study. It also contains the
 results from the SIMPER analysis conducted as part of the study.
 There are 4 SymPortal
 output files: 109_20200609_2020-06-09_11-59-06.357078.profiles.absolute.abund_and_meta.txt - Count table of ITS2 type profiles 109_20200609_2020-06-09_11-59-06.357078.seqs.absolute.abund_and_meta.txt - Count table of post-MED ITS2 sequences 2020-06-09_11-59-06.357078_braycurtis_sample_distances_A_sqrt.dist - Symbiodinium between sample braycurtis distances (with sqrt transformation of seq abundances) 109_20200609_2020-06-09_11-59-06.357078.seqs.fasta - A fasta containing the sequences referred to in the seqeunce count table. There is one multiple sequence alignment: pappas_weber_alignment.fasta There is one SIMPER output simper_output_sqrt.csv - The first index column gives the site comprarison (degree latitude of the given site as an integer are used). The second refers to a specific sequence.