For Eunicea and Leptogorgia, the museum doesn’t have significant collection of the species with annotated genomes. However, they may have more abundant material from a close relative. To check this, I searched the collections inventory for the two genera, including a filter for only collections that were preserved and stored “Dry”, and downloaded the results as CSVs. I also did the same for G. ventalina to get a sense of how many specimens we have of this species across a range of collection dates.
# Loadlibrary(dplyr)
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
library(ggplot2)G_ventalina <-read.csv("./data/G_ventalina_nmnhsearch-20250707155748.csv")Eunicea <-read.csv("./data/Eunicea_nmnhsearch-20250707190456.csv")Leptogorgia <-read.csv("./data/Leptogorgia_nmnhsearch-20250707205311.csv")# format data# Extract year from the inconsistently formatted "Date.Collected" column# This command should just extract the first 4-digit number in each entryG_ventalina$Year.Collected <-as.numeric(sub(".*(\\d{4}).*", "\\1", G_ventalina$Date.Collected))Eunicea$Year.Collected <-as.numeric(sub(".*(\\d{4}).*", "\\1", Eunicea$Date.Collected))Leptogorgia$Year.Collected <-as.numeric(sub(".*(\\d{4}).*", "\\1", Leptogorgia$Date.Collected))# Reduce scientifc names to just species namescleaned_Eunicea <-gsub("\\s*\\([^\\)]+\\)", "", Eunicea$Scientific.Name)Eunicea$Species.Clean <-sub("^((\\S+)\\s+(\\S+)).*$", "\\1", cleaned_Eunicea)cleaned_Leptogorgia <-gsub("\\s*\\([^\\)]+\\)", "", Leptogorgia$Scientific.Name)Leptogorgia$Species.Clean <-sub("^((\\S+)\\s+(\\S+)).*$", "\\1", cleaned_Leptogorgia)# Check one of the year columns#head(G_ventalina %>% select(Date.Collected, Year.Collected))
ggplot(Eunicea, aes(x = Year.Collected)) +geom_histogram(binwidth =10, boundary =1850, fill ="steelblue", color ="black") +xlab("Year Collected") +ylab("Number of Entries") +theme_minimal() +facet_wrap(~Species.Clean)
ggplot(Leptogorgia, aes(x = Year.Collected)) +geom_histogram(binwidth =10, boundary =1850, fill ="purple4", color ="black") +xlab("Year Collected") +ylab("Number of Entries") +theme_minimal() +facet_wrap(~Species.Clean)
Looks like the three species in the Eunicea and Leptogorgia genera with decent number of specimens are:
E. flexuosa
E. tourneforti
L. alba
ggplot(Eunicea[Eunicea$Species.Clean %in%c("Eunicea flexuosa","Eunicea tourneforti"),], aes(x = Year.Collected)) +geom_histogram(binwidth =10, boundary =1850, fill ="steelblue", color ="black") +xlab("Year Collected") +ylab("Number of Entries") +theme_minimal() +facet_wrap(~Species.Clean)
ggplot(Leptogorgia[Leptogorgia$Species.Clean =="Leptogorgia alba",], aes(x = Year.Collected)) +geom_histogram(binwidth =10, boundary =1850, fill ="purple4", color ="black") +xlab("Year Collected") +ylab("Number of Entries") +theme_minimal()
Both of the Eunicea species have multiple specimens from the turn of the century (~1900) and from modern collections, so I’ll take a look at the corals themselves to try to get a sense of material quantity/quality. For the potentially promising Leptogorgia (L. alba), there’s only one specimen from before 1900, and none within the last 25 years, so we wouldn’t be able to cover multiple timepoints. I’m going to exclude Leptogorgia spp. from consideration.
Also check availability of G. ventalina.
ggplot(G_ventalina, aes(x = Year.Collected)) +geom_histogram(binwidth =10, boundary =1880, fill ="steelblue", color ="black") +xlab("Year Collected") +ylab("Number of Entries") +scale_x_continuous(breaks =seq(1860, 2020, by =20)) +scale_y_continuous(breaks =seq(0, 20, by =2)) +theme_minimal()
Observations from collections search:
E. flexuosa
All dried specimens have retained natural color (rust-brown), confirming they were not bleached in the preservation process – this is ideal for us!
Abundant material from late-1800s (~1885-1900) collections. 15-20 individuals, most specimens are quite large, ~1ft in diameter.
Quite a bit of material from mid-1900s (1945-1959), with ~15 large individuals
A ton of material from collections between 1960 and 1972, ~30 large specimens, some very large. This might be an ideal “middle” timepoint.
The only “modern” collections I see are 6 specimens collected in in the last 25 years (2000, 2002, 2004, and 2019), and they’re all very small, just a couple inches in length and not fully branching. I’d have to be very careful and judicious when subsampling these.
E. tourneforti
Note
In the museum database, there are two different attributions used for E. tourneforti:
Is there a difference? Has the species been revised?
E. tourneforti may be a better Eunicea species to work with because it is more closely related to the species for which we have a high-quality genome, E. knighti (Sarmiento et al. (2025))
Eunicea phylogeny (maximum likelihood, based on reduced representation sequencing) (Sarmiento et al. 2025)
The branches of E. tournefortini are much thicker than those of E. flexuosa, which may prove beneficial for successfully extracting DNA
Several specimens (5-10) from the turn of the century, all of a good size (6-12 inches in length, branching)
~30 specimens from 1960s and 1970s, all with plenty of material (~1ft in length, branching). As with E. flexuosa, this seems like an ideal “mid-age” timepoint.
6 from early 2000s collections (2002, 2009). All are quite small, just a few inches in length and not very branched. Two, however, are quite thick, so contain more material.
Another 6 from 2019 collection (thanks Prof McFadden!). As in others, these specimens are short (~3 inches) and unbranched, but much thicker than the E. flexuosa counterparts. One is actually a bit larger too, ~6 inches long and forked.
G. ventalina
Little material from turn-of the century. I saw 2 specimens from before 1900, and both were very small, maybe 2 inches in diameter – I would be really worried about destructively sampling these, expecially because the lacy growth form of G. ventalina means there’s less tissue by surface area, so I may need to take more. There were 3 specimens from early 1900s, and these were larger (6-12 inches in diameter). One, however, was almost white – a contrast to the dark purple color of the other specimens – which suggested to me it may have either been treated (i.e. bleached) or more degraded.
As in the other species, plenty of specimens (30-40) and material (~1ft in diameter) from the 1960s and 70s.
Very little modern material, I only saw 2-3 small specimens from the early 2000s.
Conclusions
We don’t have a sufficient range of collection dates of any Leptogorgia species, and both the very old and very recent specimens of G. ventalina are potentially too small for subsampling. This leaves one of the Eunicea species, using the E. knighti genome as reference. Both E. flexuosa and E. tourneforti have sufficient material from an appropriate range of collection dates. However, E. tourneforti is more closely related to our reference E. knighti; has more specimens and material available for the critical modern reference; and is thicker, potentially providing more tissue for extraction. Because of these considerations, I think E. tourneforti is the best choice!
References
Sarmiento, Adriana, Iván Calixto-Botía, Tatiana Julio-Rodríguez, Andrea M. Quattrini, and Juan A. Sánchez. 2025. “Uncovering the Evolutionary History in Lineage of Caribbean Octocorals: Phylogenomics Reveals Unrecognized Diversity in Eunicea.”Diversity 17 (3). https://doi.org/10.3390/d17030173.
