Save annotated copy of E. tourneforti sample sheet to load to Google sheets. This is where I will keep track of what samples I am using, and their progress (subsampled, extracted, etc.)
# Loadlibrary(dplyr)
Warning: package 'dplyr' was built under R version 4.2.3
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Eunicea <-read.csv("./data/Eunicea_nmnhsearch-20250707190456.csv")# format data# Extract year from the inconsistently formatted "Date.Collected" column# This command should just extract the first 4-digit number in each entryEunicea$Year.Collected <-as.numeric(sub(".*(\\d{4}).*", "\\1", Eunicea$Date.Collected))
Warning: NAs introduced by coercion
# Reduce scientifc names to just species namescleaned_Eunicea <-gsub("\\s*\\([^\\)]+\\)", "", Eunicea$Scientific.Name)Eunicea$Species.Clean <-sub("^((\\S+)\\s+(\\S+)).*$", "\\1", cleaned_Eunicea)# Grab just E. tournefortiE_tourneforti <- Eunicea[Eunicea$Species.Clean =="Eunicea tourneforti",]write.csv(E_tourneforti, "./output/2025_07_09_subsampling_extractions/E_tourneforti_specimens.csv")
Chose the “time points” of specimen collection dates based on availability and collection location. Since both old (>100 yo) and modern (<25 yo) specimens are limited, will be sampling all of those available (~10 specimens each). There is a high number of specimens collected in the 1960s and 1970s (50-60 yo), and these specimens are quite large, providing abundant material, so this will be my “midpoint”. Since both the oldest and most recent collections were mostly performed in the Florida/Bahamas region of the Caribbean (see last post for geographic distribution details), I will also endeavor to select 1960s-1970s specimens collected from the same region.
Selected ~10 specimens from each rough time period of collection
Couldn’t find two of the old specimens (noted below). Emailed Andrea their catalog numbers.
Found 2 E. tayrona specimens that were misplaced in the E. tourneforti drawers while pulling specimens. I replaced them in the E. tayrona drawer. USNM 101774 was found in R19, C334, D11, and USNM 1018426 in R19, C334, D05. both were moved to E. tayrona drawer, R19, C334, D05.
USNM 14366 has two entries in the inventory database, but only one bag of specimens in the collection
USNM 14366 and USNM 14399 both have multiple individuals in the single specimen bag. In neither case were individuals separately labelled, so I just subsampled one of those at the top of the bag.
Extractions
Began digestions. Digestions unfortunately split over two days because I couldn’t access LAB after I finished the last of the subsampling.
Extractions performed with Qiagen DNEasy Kit. Protocol slightly modified for use with archival dried coral specimens.
Digestion Protocol:
Begin with small, cut/crushed quantity of dried tissue in a 1.5mL snap-cap tube.
Add 180uL Buffer ATL and 40uL proteinase K*. Mix by vortexing and incubate at for ~48hr* on a heated shaker, set to 56C and 80 RPM.
* indicates modification to standard protocol
First round of digestions began incubating 7/9/2025 at 5:00pm: