DOI: 10.5061/dryad.cfxpnvxhs
title: Temporal effects of preservation on the shape and size of yellow perch: Implications for morphological analyses

description: Long-term preservation of fishes often involves fixation in formalin
 followed by preservation in ethanol. This preservation technique can alter
 the shape and size of specimens, although the effects are often species
 and stage specific. In this study, we evaluated the temporal effects of
 preservation on shape and body size of adult Yellow Perch (Perca
 flavescens). We sampled 42 Yellow Perch from three lakes directly
 connected to Lake Michigan, USA. Upon capture, fish were transported to
 the laboratory, fixed in formalin, and then preserved in ethanol.
 Measurements (length, mass, and photograph to analyze shape) were made on
 fresh fish (i.e., prior to preservation) and 21, 47, and 61 days after
 being preserved in ethanol. Shape was analyzed using geometric
 morphometrics. We identified significant changes in shape and to a lesser
 degree size. The most significant shape change occurred in the comparison
 of pre-preserved vs. 21 days, with most of this variation attributed to
 dorsal bending. Shape changed slightly when comparing 21- vs. 47-days but
 was not detectable between 47- and 61-days post preservation. Total length
 and to a lesser degree centroid size and mass also differed over time, but
 total length and centroid size did not follow a similar pattern to shape.
 Changes in total length and mass were minor (&lt;1%) and were observed
 when comparing 47 vs. 61 days and pre-preserved vs. 21 days, respectively.
 Changes in centroid size were modest (~5%) and were observed paradoxically
 when comparing 47 vs. 61 days (similar to total length). Although most of
 the observed differences in the shape and size of adult Yellow Perch were
 slight, we recommend the conservative approach of only comparing fresh
 individuals with other fresh individuals and preserved individuals with
 other individuals preserved for the same amount of time when performing
 analyses of shape and size.
description: Physical measurements (total length and body mass) were measured
 in the lab and were recorded in Microsoft Excel. Photos for geometric
 morphometrics, and length and mass measurements within Excel spreadsheets
 were uploaded to R Programming, where they were analyzed. Landmarks were
 placed on the digital photographs in R.
description: # Temporal effects of preservation on the shape and size of yellow perch:
 Implications for morphological analyses
 [https://doi.org/10.5061/dryad.cfxpnvxhs](https://doi.org/10.5061/dryad.cfxpnvxhs) ## Description of the data and file structure Total length, wet mass, and photographs were taken at four time periods for each of the three lakes. Measurements and photographs were uploaded to R where they were further processed. .tps file label format follows two letter lake code (AL, WL, or MA) for Arcadia Lake, White Lake, and Macatawa Lake, the FishID number, the word day, followed by the day of preservation. For example, AL46day47.tps would be fish number 46 from Arcadia Lake on day 47 of preservation. Each  .tps file contains the coordinates for each of the 13 landmarks, along with the scale and FishID. ### Files and variables Files (TPS_files.zip): AL46day47.tps, AL45WK3.tps, AL45Day61.tps, AL45day47.tps, AL44day61.tps, AL45DOC.2.tps, AL44day47.tps, AL44WK3.tps, MA66day61.tps, MA47day47.tps, WL53day47.tps, AL44DOC.2.tps, WL54day61.tps, WL48day61.tps, MA65day61.tps, MA43day47.tps, WL52Day61.tps, WL50Day61.tps, WL47Day61.tps, WL45Day61.tps, WL77day47.tps, WL46Day61.tps, MA41day61.tps, WL44Day61.tps, MA68Day61.tps, WL49Day61.tps, WL41Day61.tps, MA61Day61.tps, MA56Day61.tps, MA46Day61.tps, WL77Day61.tps, MA64Day61.tps, MA42Day61.tps, MA45Day61.tps, WL53Day61.tps, MA47Day61.tps, AL61Day61.tps, WL51Day61.tps, AL56Day61.tps, AL59Day61.tps, AL54Day61.tps, MA43Day61.tps, AL49Day61.tps, AL51Day61.tps, AL46Day61.tps, MA65day47.tps, MA61day47.tps, MA58day47.tps, MA58Day61.tps, MA68day47.tps, WL43Day61.tps, AL48Day61.tps, MA56day47.tps, AL47Day61.tps, MA46day47.tps, MA44Day61.tps, AL60Day61.tps, MA45day47.tps, MA66day47.tps, MA42day47.tps, WL54day47.tps, AL62Day61.tps, MA41day47.tps, WL50day47.tps, MA64day47.tps, WL48day47.tps, MA44day47.tps, WL47day47.tps, WL45day47.tps, WL49day47.tps, AL67Day61.tps, WL52day47.tps, WL46day47.tps, WL51day47.tps, WL41day47.tps, WL43day47.tps, AL62day47.tps, AL67day47.tps, WL44day47.tps, AL61day47.tps, AL60day47.tps, AL59day47.tps, AL54day47.tps, AL56day47.tps, AL51day47.tps, AL48day47.tps, AL49day47.tps, WL77DOC.2.tps, AL47day47.tps, WL52DOC.tps, WL54DOC.tps, WL53DOC.tps, WL50DOC.tps, WL48DOC.tps, WL51DOC.tps, WL49DOC.tps, WL45DOC.tps, WL46DOC.tps, WL43DOC.tps, WL44DOC.tps, WL41DOC.tps, WL47DOC.tps, MA68WK3.tps, MA65WK3.tps, MA61WK3.tps, MA58WK3.tps, MA56DOC.tps, MA58DOC.tps, MA56WK3.tps, MA47WK3.tps, MA46WK3.tps, MA47DOC.tps, MA46DOC.tps, MA44WK3.tps, MA45DOC.tps, MA44DOC.tps, MA43WK3.tps, MA42DOC.tps, MA43DOC.tps, MA41WK3.tps, MA41DOC.tps, AL67DOC.tps, AL61DOC.tps, AL62DOC.tps, AL60DOC.tps, AL59DOC.tps, AL56WK3.tps, AL56DOC.tps, AL54WK3.tps, AL51WK3.tps, AL54DOC.tps, AL51DOC.tps, AL49WK3.tps, AL49DOC.tps, AL48WK3.tps, AL47WK3.tps, AL48DOC.tps, AL47DOC.tps, AL46WK3.tps, MA61DOC.2.tps, MA64WK3.tps, AL46DOC.tps, WL54WK3.2.tps, MA66WK3.2.tps, MA42WK3.2.tps, MA45WK3.2.tps, AL59WK3.2.tps, AL67WK3.tps, AL62WK3.tps, AL61WK3.tps, MA68DOC.tps, MA66DOC.tps, AL60WK3.tps, WL51WK3.tps, WL47WK3.tps, WL48WK3.tps, MA64DOC.tps, WL44WK3.tps, WL41WK3.tps, WL43WK3.tps, WL77WK3.tps, WL52WK3.tps, MA65DOC.tps, WL45WK3.tps, WL53WK3.tps, WL50WK3.tps, WL49WK3.tps, and WL46WK3.tps **Description:** Landmark coordinates #### File: residuals.xlsx **Description:** Used to store landmark coordinates for consensus plots ##### Variables * X - coordinate on the x-axis * Y - coordinate on the y axis * Landmark - position number * FISHID - alphanumeric identifier for each specimen * Period - days after preservation (DOC = day of capture). #### File: Master.xlsx **Description:** Used to store length and mass data ##### Variables * Observation - a unique identifier * Lake - water body each specimen was collected from * FishID - alphanumeric identifier for each specimen * Total_length (mm) - measurement of body size, measured from the tip of the snout to the end of the caudal fin * Standard_length (mm) - measurement of body size, measured from the tip of the snout to the base of the caudal fin * Pec_Length (mm) - measurement of pectoral fin size, measured from base of the pectoral fin to the tip of the pectoral fin * Weight (g) - measurement of size in grams * Notes - extra, pertinent information for each specimen * Period - days after preservation ## Code/software I used Microsoft Excel to store physical data, and processed/analyzed the data in R version 4.2.1. Packages included: *#to bring in excel data* (readxl) *#to manipulate data* (dplyr) (tidyverse) (reshape2) *#to perform geometric morphometrics* (geomorph) (Morpho) (shapes) (RRPP) (vctrs) *#To make tables:* (magick) (webshot) (knitr) (kableExtra) *#create excel spreadsheet* (openxlsx)