DOI: 10.5061/dryad.bvq83bkk6
title: A common garden of <em>Halichondria</em> sponges: taxonomic revision of Northeast Pacific Halichondriidae reveals many cryptic introduced species

description: Sponges (phylum Porifera) possess biochemical, cellular, and physiological
 traits with valuable biotechnical applications. However, our ability to
 harness these natural innovations is limited by a classification system
 that does not fully reflect their evolutionary history. In this study, we
 uncover numerous cryptic species within the genus Halichondria that are
 morphologically indistinguishable from the well-known H. panicea. Many of
 these species have habitat preferences and geographic distributions that
 strongly suggest they have been dispersed by human activity. Most of these
 species are broadly sympatric with their closest relatives, and these
 overlapping distributions allow us to use patterns of DNA variation to
 infer reproductive isolation between clades in nature. With reproductively
 isolated species thus delineated, we can use DNA states as taxonomic
 characters to formally describe them. Though much remains to be learned
 about these newly discovered species, the natural "common
 gardens" of introduced sponges in California, New York, and other
 locations provide opportunities to test hypotheses about their
 diversification in future work.
description: # A common garden of *Halichondria* sponges: taxonomic revision of
 Northeast Pacific Halichondriidae reveals many cryptic introduced species
 **Supplementary data** Access this dataset on Dryad:
 [https://doi.org/10.5061/dryad.bvq83bkk6](https://doi.org/10.5061/dryad.bvq83bkk6) ## Description of the data and file structure These files compliment this paper: [https://ssbbulletin.org/article/id/5811/](https://ssbbulletin.org/article/id/5811/) Detailed information about each file is given below. Some are bulk, raw data files, some are DNA alignments, and others are supplementary figures. ## 12 Files 1\. Table_S1_archival.csv Metadata for all samples investigated. Missing and/or irrelevent data are coded as "n/a". Most samples have two unique identifiers: a "Sample ID" that was used at the time of collection, and/or is a shortened version of a museum ID, and a "Museum voucher" which is the code used by the museum collection housing the sample. Latitude and Longitude are in decimal degrees, absent for some samples when unknown. DNA voucher numbers refer to Genbank. 2\. Raw_spicule_data.csv Measurement data from all spicules. Lengths and widths are provided for each spicule, in microns; "n/a" indicates a measurement was not taken. Each row is a spicule. Columns correspond to Species, Sample IDs (in Table S1), Length of spicule in microns, Width of spicule at widest point, in microns, when measured, and finally information about the style of spicule and/or the region of the sponge it was isolated from. "ecto/choa not separated" means that a fragment including outer and inner portions of the sponge was used for the spicule prep; "ectosome" means that this tissue was removed as cleanly as possible and prepped alone; "choanosome" means only internal tissue. 3\. Primer_sequences.csv Sequences of Sanger sequencing primers used. 4\. 28S_alignment.fasta Sequence alignment at the 28S locus. Diagnostic positions mentioned in the manuscript refer to this alignment. 5\. cox1_alignment.fasta Sequence alignment at the cox1 locus. Diagnostic positions mentioned in the manuscript refer to this alignment. 6\. full_ribosomal_alignment.fasta Sequence alignment at the full ribosomal locus. Diagnostic positions mentioned in the manuscript refer to this alignment. 7\. Mitogenes_alignment.fasta Sequence alignment of the concatenated mitochondrial genes. Diagnostic positions mentioned in the manuscript refer to this alignment. 8\. nd1_alignment.fasta Sequence alignment at the nd1 locus. Diagnostic positions mentioned in the manuscript refer to this alignment. 9\. Figure_S1_cox1.pdf Figure_S1: Phylogeny of the cox1 locus. Figure caption is in file Suppl_figures_4_to_7.docx 10\. Figure_S2_28S.pdf Figure_S2: Phylogeny of the 28S locus. Figure caption is in file Suppl_figures_4_to_7.docx 11\. Figure_S3_ND1.pdf Figure_S3: Phylogeny of the nd1 locus. Figure caption is in file Suppl_figures_4_to_7.docx 12\. Suppl_figures_4_to_7.docx Supplemental figures 4 to 7, and all supplemental figure captions