DOI: 10.5061/dryad.08kprr5cp
title: Amblema plicata microsatellite data from wild and hatchery produced populations

description: The goal of this project was to compare the genetic diversity of a wild
 source population of Three-ridge mussels (Amblema plicata) to the cohort
 of juveniles propagated from three gravid females from the wild
 population. The juveniles were subsampled directly after transformation
 from glochidia (“young juveniles”) and subsampled again after one year of
 being raised in the hatchery (“old juveniles”).  After correcting
 for different sample sizes, the young juveniles exhibited the greatest
 allelic richness, followed by the source mussels and then the old
 juveniles. All three groups exhibited private alleles. Private alleles in
 the juveniles indicated the dams (mothers) were likely fertilized by males
 living upstream of the source population, outside of the sampling effort
 of this study. High levels of multiple paternity were observed in the
 young and old juveniles. In total, 89 juveniles were estimated to have
 been sired by 58 males, increasing the amount of genetic variability in
 the produced population. The old juvenile samples were taken from a random
 subsample and were found to have been produced nearly entirely from a
 single dam, indicating differential mortality in the hatchery which
 reduced the amount of genetic variability in the released population. The
 old juvenile sample was significantly differentiated from the source
 population (p&lt;2.04e-26), suggesting the released juvenile
 population did not fully represent the source population.
description: We collected non-destructive samples from 50 Three-ridge mussels
 in the Upper Cedar River near Lansing, Minnesota using buccal swabs, which
 were then stored in ethanol (the ‘source’ sample set). Three gravid
 females from the source population were used for propagation at the Center
 for Aquatic Mollusk Programs in Lake City, MN. Hatchery staff infested
 individual walleye (<em>Sander vitreus) </em>host fish with
 the glochidia from a single dam. After transformation and dropping from
 their hosts, 20 juveniles from each dam were collected and preserved in
 ethanol for a total of 60 samples (‘young juveniles’). Staff combined the
 remaining juveniles and reared them at the hatchery for one year. On July
 22, 2020, staff collected 50 more juveniles and preserved them in ethanol
 (‘old juveniles’). Genomic DNA was isolated from the
 buccal swabs of the adult mussels using QIAGEN’s Purgene Buccal Cell Core
 Kit A following the ‘DNA Purification from a Buccal Brush’ protocol
 (Qiagen). Genomic DNA was isolated from the young juvenile samples using
 Chelex 100 Resin (BioRad) following a modified version of the protocol
 outlined in Singh, Kumari, and Iyengar (2018). Tissue samples were taken
 from the old juveniles, and genomic DNA was isolated using the QIAamp DNA
 mini kit according to the ‘Tissue’ protocol (Qiagen). All extracted DNA
 was quantified using a Nanodrop ND1000 spectrophotometer and stored at 4°
 C. We used 16 microsatellite markers developed for the Fat Threeridge
 (<em>Amblema neislerii</em>) (Díaz-Ferguson, Williams, and
 Moyer 2011) to genotype the mussel samples collected (Table 1).
 We conducted polymerase chain reaction (PCR) amplification using
 the BIOLASE PCR kit (Bioline, Boston, MA). Each 10 microliter (μl)
 reaction contained 6.6 μl of sterile deionized water, 1 μl of Biolase NH4
 reaction buffer (10x), 0.6 μl of MgCl2 (50 mM), 0.8 μl of dNTP’s (2.5 mM
 each), 0.1 μl of M13 labeled forward primer (20 mM), 0.1 μl of reverse
 primer (20 mM), 0.05 μl of M13 labeled oligo (20 mM), 0.05 μl of Biolase
 DNA Taq polymerase (5 U/ μl), and 1 μl of template DNA (approximately 2
 nanograms (ng)/ μl). Reactions were completed in Eppendorf Master Cycler
 Thermocyclers under the following conditions: 95⁰C/ 5:00 min; (94⁰C/ 00:30
 seconds, touchdown beginning at 56⁰C and dropping by 0.6⁰C per cycle/ 1:00
 minute, 72⁰C/ 00:30 seconds) x11; (94⁰C/ 00:30 seconds, 55⁰C / 1:00
 minute, 72⁰C/ 00:30 seconds) x25; 72⁰C / 20:00 minutes. A negative control
 was performed with each reaction. PCR products were visualized on 1.5%
 agarose gels against a 100 bp DNA ladder to confirm the success of the
 reactions and to ensure the negative control showed no contamination.
 Allele sizes were determined with capillary electrophoresis on an Applied
 Biosystems 3500 Genetic Analyzer by the Iowa State University DNA
 Facility. We scored raw data with the software Gene Marker (Version
 3.0.1). We checked all loci for null alleles with MICRO-CHECKER (Van
 Oosterhout et al. 2004). Loci with possible null alleles were excluded
 from the data set.
description: # Amblema plicata microsatellite data from wild and hatchery produced
 populations
 [https://doi.org/10.5061/dryad.08kprr5cp](https://doi.org/10.5061/dryad.08kprr5cp) ## Description of the data and file structure The data was collected to do a genetic comparison of a wild source population of Three-ridge mussels ('source') to the juvenile population propagated from the source. The propagated juveniles were subsampled at two points in time, once directly after transformation from glochidia ('J1'), and again after being reared for a year in the hatchery ('J2'). ### Files and variables #### File: Ampl\_3pops\_2019.csv **Description:**  This data is formatted for GenAlEx. 0s indicate no data-- either the locus did not amplify or the data was removed later due to null alleles.  ##### Variables * 10: The number of loci. * 134: Total number of samples.  * 3: Number of 'populations'-- source (wild mussels), J1 (juveniles directly after transformation from glochidia), J2 (juveniles after a year in the hatchery) * 45: Sample size of source * 41: Sample size of J1 * 48: Sample size of J2 ## Code/software The data can be opened in any spreadsheet or text editor software. Microsoft Excel is recommended, as the data is formatted to be read by the GenAlEx software that can be added in to Excel.