Pelvic spine reduction affects diet but not gill raker morphology in two polymorphic brook stickleback (Culaea inconstans) populations

Pelvic spine polymorphism occurs in several species in the stickleback family (Gasterosteidae). Given parallel selection driving similar phenotypic polymorphisms in multiple stickleback species, we sought to determine the extent of parallelism in the ecological consequences of pelvic spine reduction. Based on a metabarcoding analysis of brook stickleback gut contents in two polymorphic populations, we found a shift towards a planktonic diet was associated with pelvic spine reduction. These results contrast with those found in threespine stickleback where pelvic spine reduction is associated with a shift towards a benthic diet. Hence, we found non-parallel consequences of spine polymorphism across species. Furthermore, a change in gill raker morphology has been consistently implicated in the change in diet in pelvic-reduced threespine stickleback. But we found no evidence of any difference in gill raker morphology associated with pelvic spine polymorphism in brook stickleback., Brook stickleback were collected in Alberta, Canada, from Muir Lake (UTF-8 encoded WGS84 latitude and longitude: 53.627659, -113.957524) and Shunda Lake (52.453899, -116.146192).
For gut content metabarcoding: Fish guts collected from 95 fish in 2019 were shipped to the Canadian Centre for DNA Barcoding at the University of Guelph for membrane-based DNA extraction and amplicon sequencing. This metabarcoding approached used five PCR primer sets designed to amplify a barcode region of the cytochrome c oxidase subunit I (COI) gene in arthropods, mollusks, annelids, amphipods, and microalgae (details of COI amplification can be found at http://ccdb.ca/site/wp-content/uploads/2016/09/CCDB_Amplification.pdf). A second round of PCR amplification added Ion Torrent sequencing adapters and a unique multiplex identifier (MID) sequence to the 5’ end of amplicons for each sample. Amplified COI fragments were then pooled and single-end sequenced on an Ion Torrent PGM sequencing platform (Thermo Fishe..., For gut content metabarcoding: We removed primer and adapter sequences from the de-multiplexed reads, and discarded reads that consisted of only primer or adapter sequence using CUTADAPT v2.3. We used DADA2 in R v4.2.2 to trim and filter reads, estimate error rates for the filtered and trimmed amplicon dataset, combine identical reads into unique sequences, and infer biologically meaningful (as opposed to spurious) amplified sequence variants (ASVs). We exported the list of ASVs across all samples to a fasta file and used the JAMP pipeline in BOLDigger to identify the best-fitting taxonomic identification for each ASV. We used the PHYLOSEQ package to create a data object in R that allowed us to associate the abundance of each taxon identified in each fish’s gut with other sample data (i.e. lake, sex, size, and pelvic phenotype). We used the DESeq2 package in R to conduct Wald tests of the Log2 fold-differences in the abundances of each eukaryote family in the diets of brook stickleback...., # Pelvic spine reduction affects diet but not gill raker morphology in two polymorphic brook stickleback (Culaea inconstans) populations

***

The data consist of two files - one is a zip archive of sequence data from metabarcoding of brook stickleback gut contents, and one is a csv file of measurements and counts of brook stickleback gill rakers. In addition, there is a separate \"metadata\" csv file associated with the metabarcoding dataset, which includes the phenotype, sex, size, and population information for each individual in the metabarcoding dataset (this sample information is included as columns in the csv file for the gill raker dataset).

## Description of the data and file structure

Mee\_etal\_CCDB\_Culaea\_guts\_metabarcoding.zip - This zip archive contains fastq files with the sequence information from 95 brook stickleback guts.

Metadata\_culaea\_gut.csv - this csv file has all the sample information (e.g. sex, pelvic phenotype, length, population) for all 95 brook stickl...