Below, you will find all data included in Gunn et al. (2024). These data can be used along with the associated project GitHub repository to work through all data analyses step-by-step.

Project: Effects of admixture on fitness in Neosho Bass populations

We assessed the effect of admixture on fitness in two stream populations within the native range of the Neosho Bass (M. velox; NB) which are known to have extensively hybridized with Smallmouth Bass (Micropterus dolomieu; SMB). Specifically, we used 14 microsatellite loci in a Bayesian analysis of population structure to estimate proportions of interspecific ancestry in individuals collected from Big Sugar Creek and the Elk River in southwestern Missouri (Central Interior Highlands ecoregion (CIH), North America). We used ancestry inference to estimate the proportion of ancestry derived from SMB and NB. For each individual, we measured age and total length and projected individual growth using the standard parameterization of the von Bertalanffy growth model. Finally, we used body condition as a proxy for fitness and generated an ancestry-condition correlation across the global dataset. We ultimately sought to understand the short-term genetic consequences of admixture for NB populations in order to better inform management and long-term viability of distinct, economically and ecologically important sportfish species in the CIH.

Data

In this repository, you will find three separate data files (each file is provided both in comma separate value format, i.e., .csv, and Excel format, i.e., .xlsx). Files in .csv format are provided for machine readability, but all corresponding code requires files in .xlsx format for analysis. We also provide one data folder. Files and folders are required to reproduce analyses for Gunn et al. (2024):

1. raw genotype data (genotype_data.csv; genotype_data.xlsx)
2. raw phenotype data (phenotype_data.csv; phenotype_data.xlsx)
3. metadata (metadata.csv; metadata.xlsx)
4. raw otolith images (otolith_images.zip)

Below, we provide a full description of each data file and folder, including names and descriptions of variables in each column.

genotype_data.csv (.xlsx)

1. "sample_id": a unique, alphanumeric ID for each sample
2. "structure_number": the alphanumerical ID for each individual in the proper format for analysis with the program STRUCTURE
3. *locus**names: for each microsatellite locus used in this study, there are two adjacent columns, the first labeled with the locus name (e.g., "mdo9", "mdo5", "mdo7", "*mdo10", etc.) and the second with no header label (blank). Each column contains one of two alleles at that locus (three-digit numerical value, e.g., 146). *Note: columns with blank headers must remain blank, as they will be read and transformed using the R library employed for analysis of these data.

phenotype_data.csv (.xlsx)

1. "sample_id": same as in metadata and genotype data (followed by "structure_number"; see Analysis 3, Phase 1, step 1e)
2. "sex": male or female, determined by internal gonad examination,
3. "tl_alive": total length (mm) of the fish immediately upon capture by rod-and-reel, as measured from the tip of the lower mandible to the posterior tip of the caudal fin squeezed together
4. "tl_dead": total length (mm) of the fish upon sample processeing (after approximately one month frozen)
5. "mass_dead": mass (g) of the fish in grams at time of sample processing
6. "meas_ints": initials of the person doing the phenotypic measuring, measuring, or assessment, for later analysis of observer/measurement bias
7. "eddie_age": age estimate based on sagittal otolith annuli, performed by Eddie Sterling
8. "joe_age": age estimate performed by Joe Gunn
9. "michael_age": age estimate performed by Michael Moore
10. "consensus_age": ultimate age estimate based on consensus of three agers, Eddie, Joe, and Michael
11. "sl": standard length (mm) of the fish, as measured from the tip of the mandible to the hyperal plate, just anterior to the caudal fin
12. "bd": body depth (mm) , as measured at the thickest part of the fish
13. "hl": head length (mm), as measured from the tip of the lower mandible to the posterior end of the gill plate
14. "ol": orbital length (mm) , the diameter of the eye ball
15. "sd_ray": the number of soft dorsal fin rays.

metadata.csv (.xlsx)

1. "sample_id": a unique, alphanumeric ID for each sample
2. "river_code": the alphabetical prefix for each sample id, where "FBS" stands for "Fitness, Big Sugar Creek" and "FER" stands for "Fitness, Elk River"
3. "sample_number": the numerical prefix for each sample (01, 02, 03,..., 71)
4. "structure_number": the alphanumerical ID for each individual in the proper format for analysis with the program STRUCTURE
5. "easting": easting UTM (ZONE 15S) measurement (GIS)
6. "northing": northing UTM (ZONE 15S) measurement (GIS)
7. "dist_from_df": distance (m) from Deep Ford Access (DFA) at which each sample was collected
8. "range_id": species native range from which each individual was collected
9. "river": river or stream from which each individual was collected
10. "population": designation for whether the sample was included in growth analyses ("sample") or was used solely as a reference for ancestry analysis ("reference")

NA - not available

otolith_images.zip

Compressed (zip) folder containing all raw otolith images (PNG) analyzed in this study. Images are labeled as described for the "sample*id" column of each raw dataset (genotype_data phenotypes_data, metadata), i.e., with a unique alphanumeric ID representing the fish from which the otolith was collected.

To reproduce analyses for Gunn et al. (2020), follow instructions in the README.md file on the project Zenodo repository (https://doi.org/10.5281/zenodo.13983316). First, download these data into your /raw_data directory within the home working directory. You should then be ready to fully analyze data as described in the associated Rmarkdown files.

If you have any questions or issues with data and/or code, please don't hesitate to contact me: jcgunn@uvm.edu

Versioning

Oct 23, V2: Added image folder and csv versions of all Excel files