michaeltconnelly/pocillopora_hdna_uces

Data and scripts for analysis of dry coral hDNA extractions and UCE sequencing

pocillopora_hDNA_uces

This repository holds the data and code for analysis of historical DNA (hDNA) sequenced from dried Pocillopora corals in the Smithsonian National Museum of Natural History dry collections. The manuscript detailing the results of these experiments is now published in Coral Reefs!

Please visit: "Unlocking the treasure trove: leveraging dry coral specimens for museum genomics", Connelly et al. (2024)

Catalog Number	Origin	Collection Date	Age (years)	UCE loci	GSH	Current Nomenclature
USNM 1199340	Ecuador	May 19, 1966	58	799	GSH09c_TSP	P. grandis
USNM 1260713	Ecuador	September 21, 1966	58	795	GSH09c_TSP	P. grandis
USNM 1208931	Egypt	June, 1987	37	1495	GSH13a	P. verrucosa
USNM 1260710	Madagascar	October 23, 1964	60	1173	GSH13a	P. verrucosa
USNM 1260508	Mexico	March 1, 1934	90	1504	GSH09c_TSP	P. grandis
USNM 1260495	Panama	April 30, 1971	53	814	GSH09c_TSP	P. grandis
USNM 81557	Tanzania	August 16, 1957	67	327	GSH05a-3	P. acuta

For more information on specimens, visit https://collections.nmnh.si.edu/search/iz/

Raw sequencing reads are available in the NCBI SRA under accessions PRJNA1075782 for historical specimens and PRJNA1055517 and PRJNA1076507 for contemporary samples.

(A) IQ-TREE maximum likelihood phylogenetic tree depicting the placement of NMNH IZ Pocillopora specimens (in red) in the context of publicly available reference genomes (in blue), genomic species hypotheses (GSHs, in green), and contemporary specimens. The tree was constructed with a 50% sample occupancy matrix containing 1,510 UCE loci, 600,934 bp, and 37,584 informative sites, and nodes with <90% bootstrap support are labelled. (B) Photographs of NMNH IZ Pocillopora specimens that were successfully sequenced (>300 UCE sequences) and placed onto the ML phylogeny.