DOI: 10.5061/dryad.tb2rbp07q
title: Supplementary data for: simultaneous species detection and discovery with environmental DNA metabarcoding: a freshwater mollusk case study

description: Environmental DNA (eDNA) sampling is a powerful tool for rapidly
 characterizing biodiversity patterns for specious, cryptic taxa with
 incomplete taxonomies. One such group that are also of high conservation
 concern are North American freshwater gastropods. In particular,
 springsnails of the genus Pyrgulopsis (Family: Hydrobiidae) are prevalent
 throughout the western United States where &gt;140 species have been
 described. Many of the described species are narrow endemics known from a
 single spring or locality and it is believed that there are likely many
 additional species which have yet to be described. The distribution of
 these species across the landscape is of interest because habitat loss and
 degradation, climate change, groundwater mining, and pollution have
 resulted in springsnail imperilment rates as high as 92%. Determining
 distributions with conventional sampling methods is limited by the fact
 that these snails are often &lt;5 mm in length with few distinguishing
 morphological characters, making them both difficult to detect and to
 identify. In order to facilitate detection of Pyrgulopsis we developed an
 eDNA metabarcoding protocol that is both inexpensive and capable of rapid,
 accurate detection of all known Pyrgulopsis species. When compared with
 conventional collection techniques, our pipeline consistently resulted in
 detection at sites previously known to contain Pyrgulopsis springsnails
 and at a cost per site that is likely to be substantially less than the
 conventional sampling and individual barcoding that has been done
 historically. Additionally, because our method uses eDNA extracted from
 filtered water it is non-destructive and suitable for the detection of
 endangered species where “no take” restrictions may be in effect. This
 effort represents both a tool which is immediately applicable to a group
 of high conservation concern across western North America and a case study
 in the broader application of eDNA sampling for landscape assessments of
 cryptic taxa of conservation concern.
description: Dataset includes a 137 taxa alignment of COI sequences in FASTA
 format.  Sequences were obtained from Genbank, accessions provided in
 taxon name.  Sequences were aligned using MAFFT 7.215 then partitioned by
 codon.  The corresponding partion file is provided as well
 (partition_file.nex). Additionally, this dataset contains the Maximum
 likelihood phylogeny (Supplementary_Figure_1_SVG.svg) estimated from this
 alignment using IQTree 2.1.3 with the following command line:
 iqtree2 -s <em>Alignment_file.fa</em>  -p
 <em>partition_file.nex</em> -runs 15 -m MFP+MERGE -B 1000 -nt
 2.
description: # Supplementary Data for: simultaneous species detection and discovery
 with environmental DNA metabarcoding: a freshwater mollusk case study
 ## Description of the data
 and file structure Dataset includes a 137 taxa alignment of COI sequences
 in FASTA format (Alignment_file.fa).  Sequences were obtained from
 Genbank, accessions are provided in taxon name.  Sequences were aligned
 using MAFFT 7.215 with default settings. The alignment was then
 partitioned by codon with each codon position modeled separately in the
 likelihood analysis described below. Included is the partition_file.nex
 file used to define these codon positions. Additionally, this dataset
 contains the Maximum likelihood phylogeny estimated from this alignment
 using IQTree 2.2.1 with the following command. command line: iqtree2 -s
 *Alignment_file.fa*  -p *partition_file.nex* -runs 15 -m MFP+MERGE -B 1000
 -nt 2 Data was derived from the following sources: * NCBI GenBank
 (*[Nucleic Acids
 Research](https://www.ncbi.nlm.nih.gov/pubmed/23193287)*[, 2013
 Jan;41(D1):D36-42](https://www.ncbi.nlm.nih.gov/pubmed/23193287))