A common garden of Halichondria sponges: taxonomic revision of Northeast Pacific Halichondriidae reveals many cryptic introduced species
Data files
Nov 06, 2025 version files 4.55 MB
-
28S_alignment.fasta
710.80 KB
-
cox1_alignment.fasta
632.50 KB
-
full_ribosomal_alignment.fasta
715.05 KB
-
Mitogenes_alignment.fasta
1.69 MB
-
nd1_alignment.fasta
157.83 KB
-
Primer_sequences.csv
557 B
-
Raw_spicule_data.csv
573.23 KB
-
README.md
3.04 KB
-
Table_S1_archival.csv
58.05 KB
Abstract
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.
Supplementary data
Access this dataset on Dryad: 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/
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
