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Flexibility in Red Sea Tridacna maxima-Symbiodiniaceae associations supports environmental niche adaptation datasets

Cite this dataset

Hume, Benjamin et al. (2021). Flexibility in Red Sea Tridacna maxima-Symbiodiniaceae associations supports environmental niche adaptation datasets [Dataset]. Dryad.


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.


The SymPortal files were output directly from the remote instance of SymPortal.

The SymPortal Files are:





The pappas_weber_alignment.fasta was created as such:

Reanalysis of ITS1-5.8S-ITS2 haplotypes from previous characterizations          
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 ( 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 Symbiodinium sequences with site as the grouping factor. Conducted in Python, we used ecopy’s simper function.

Usage notes

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:


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.