DOI: 10.5061/dryad.gqnk98sz7
title: Population genetics and origins of rainbow smelt (Osmerus mordax) in the Laurentian Great Lakes

description: Rainbow smelt (Osmerus mordax) are a small predatory fish first recorded
 in the Great Lakes in 1906. Despite the major ecological and economic
 impacts of smelt in the Great Lakes, most information on the origins of
 these populations comes from second-hand accounts written decades after
 the first smelt were recorded. These accounts are based on circumstantial
 evidence and include speculation about natural migration and reproduction
 of smelt in Lake Ontario as well as secondary anthropogenic introductions
 Great Lakes. Here, we use mtDNA sequencing and RFLP to demonstrate that
 the single, recorded government introduction of smelt to the Great Lakes
 in Michigan around 1912 accounts for only about half of the ancestry of
 Great Lakes smelt. The remaining ancestry appears to be from an anadromous
 source population. Furthermore, the absence of a longitudinal cline in
 haplotype frequency indicates that gene flow and dispersal are high
 amongst smelt in the Great Lakes. Our results suggest a multiple invasion
 pathway within the Great Lakes and provide insights into the genetic
 diversity of the extant Great Lakes populations.
description: All of the clade data were collected using RFLP. As outlined in
 the manuscript, some of the analyses were followed up with sequencing, and
 this data is also included. Rainbow smelt were
 collected from Lake Ontario, Lake Erie, Jesse Lake, Wawa Lake, Wanapitei
 Lake, and Lake Nipigon. Coordinates are given in the haplogroup
 table. <em>Laboratory
 analysis</em> The total length of each thawed
 trawl-caught fish was recorded in millimetres, nose-to-tail. DNA
 extraction was performed using Proteinase K (Thermo Fisher, Waltham, USA)
 digestion followed by successive phenol and chloroform-isoamyl alcohol
 extraction steps, or by the DNeasy Blood and Tissue Kit (QIAGEN, Hilden,
 Germany). PCR amplification of mitochondrial NADH subunit 6 (ND6) was
 performed following the protocol of Pigeon et al. (1998). Primers used
 were ND56R250 (ACTGGTCGTGTTTGTATAC) and ND56R450V
 (GGACTACAAACAAAGTCAATAAG). This resulted in the amplification of a 288 bp
 amplicon, which was then incubated for 3 hours at 37°C in Tango buffer
 (Thermo Fisher, Waltham, USA) with the restriction enzyme DDeI (Thermo
 Fisher, Waltham, USA), according to the manufacturer’s usage
 directions. For a subset of the smelt, Sanger
 sequencing was performed on the mitochondrial NADH subunit 5 (ND5) gene. A
 911 bp fragment beginning at position 965 of NCBI Accession AF034752.1.1
 was amplified using 21-base primers designed for this study, FWD_911
 (TTGGCCTCAATCAACCTCAGC) and REV_911 (GCTAACTCGGGGGTTAAGTCG). Our
 thermocycler program was a modified version of Pigeon et
 al.’<em>s</em> (1998) protocol with a 1-minute extension time.
 835 bp of consensus sequence was retained from these reads.
description: # Population Genetics and Origins of Rainbow Smelt (*Osmerus mordax*) in
 the Laurentian Great Lakes
 [https://doi.org/10.5061/dryad.gqnk98sz7](https://doi.org/10.5061/dryad.gqnk98sz7) ## Description of the data and file structure hijop.csv contains all the haplotypes found, props.csv lists the proportions of each clade in each sampling location, and clades_for_lengths.csv lists the lengths of the fish from each clade used for the size comparison analysis. ### Files and variables #### File: hijop.csv **Description:**  Haplotypes from our study ##### Variables * Haplotype Name: Arbitrary designation meant to denote each haplotype with a single letter (e.g. Haplotype O was found in all sites) * Haplotype: DNA sequence of haplotype * Frequency: Count of the haplotype in all sampling locales, including reference populations in Quebec and Mass. * Specimens: List of specimens with each haplotype. Codes consist of sampling site, and then a numerical identifier (e.g. 1, 01, x01, 01-1). * OSW = Oswego * EB = East Basin Lake Ontario * E40/E16 = East Basin Lake Erie * MTN = Mtn Bay, Lake Superior * WAWA = Wawa Lake * WAN = Wanapitei * NIPIGON = Nipigon * RichelieuRiver = Richelieu River * JDA/JDB = St. Lawrence Estuary * BostonFore = Fore River * SNP: refers to SNP TGA(A/G)GCC, used to determine clade and verify results of RFLP. A = Atlantic, G = Acadian #### File: props.csv **Description:** Geographical distribution of clades ##### Variables * Region: Sampling site. East Basin = East Basin of Lake Ontario * Acadian : Count of Acadian clade smelt * Atlantic: Count of Atlantic clade smelt * Latitude: Latitude of sampling site * Longitude: Longitude of sampling site #### File: clades_for_lengths.csv **Description:** Sizes for trawl caught fish ##### Variables * Code: Individual identifier of smelt * Region: Sampling site: East Basin [of Lake Ontario]; Lake Erie; Oswego (Lake Ontario) * Total length (mm): Length from nose to tip of tail. "na" indicates samples for which no measurements could be taken. * Haplogroup: Atlantic or Acadian clade ## Code/software You can use Microsoft Excel (2021) or Google Sheets to view the data, however for our analyses we used pandas 2.2.3, seaborn 0.13.2 and scipy 1.15.0 in Python 3. T-test calculations for difference in smelt lengths between clades followed the format: ``` import scipy.stats as stats import seaborn as sns sns.boxplot(x='Haplogroup', y='Total length (mm)', data=df).set(title='Ontario and Erie') plt.show() stats.ttest_ind(a=df["Total length (mm)"][df.Haplogroup == "Acadian"], b=df["Total length (mm)"][df.Haplogroup == "Atlantic"]) ``` ## Access information Other publicly accessible locations of the data: * Lac St. Jean mtDNA template: [https://www.ncbi.nlm.nih.gov/nuccore/NC_015246.1?report=genbank](https://www.ncbi.nlm.nih.gov/nuccore/NC_015246.1?report=genbank)