TY - JOUR
T1 - Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama
AU - Sullivan, Alexis P.
AU - Marciniak, Stephanie
AU - O'Dea, Aaron
AU - Wake, Thomas A.
AU - Perry, George H.
N1 - Funding Information:
We thank Ashley Sharpe, Nicole Smith-Guzman, Suzette Flantua, Jarrod Scott, Matthieu Leray, and Wilmer Elvir for their assistance in live conch collection, and Brigida de Gracia for assisting with the planning and coordination at the STRI Naos Marine and Molecular Laboratories. We also thank the Bocas del Toro Research Station team, especially Plinio Góndola and Urania González. Thank you, Marian Shaffer and Felix Rodriguez, for helping to collect the paleontological conch, as well as Marco and Fausto Alvarez, Annick Belanger, and the staff at Sweet Bocas who kindly gave logistical support. Permits to collect were provided by three Panamanian ministries; Ministerio de Comercio e Industria (MICI), MiAmbiente, and El Ministerio de Cultura de Panamá (formerly Instituto Nacional de Cultura, INAC). We thank the Dirección Nacional del Patrimonio Histórico, Instituto Nacional de Cultura, Republica de Panamá for issuing Resolución 153-14, permitting the excavation of units 60 and 61 at Sitio Drago and the Serracín family for access to the site – especially Juany and Willy Serracín and Ana Serracín de Shaffer. We also thank Daniel Schussheim for machining the shell smasher, the NYU Langone Genome Technology Center for sequencing our libraries, and Christina Bergey, Kathleen Grogan, and the other members of the Perry Lab for their discussion and analytical advice. Components of this work were supported by the National Science Foundation Graduate Research Fellowship program (DGE-1255832, to A.P.S.), a grant from the National Science Foundation (BCS-1554834 to G.H.P.), the Smithsonian Tropical Research Institute Short-Term Fellowship Program (to A.P.S.), and the SNI program from the Secretaría Nacional de Ciencia y Tecnología e Innovación, Panamá (to A.O.).
Funding Information:
We thank Ashley Sharpe, Nicole Smith‐Guzman, Suzette Flantua, Jarrod Scott, Matthieu Leray, and Wilmer Elvir for their assistance in live conch collection, and Brigida de Gracia for assisting with the planning and coordination at the STRI Naos Marine and Molecular Laboratories. We also thank the Bocas del Toro Research Station team, especially Plinio Góndola and Urania González. Thank you, Marian Shaffer and Felix Rodriguez, for helping to collect the paleontological conch, as well as Marco and Fausto Alvarez, Annick Belanger, and the staff at Sweet Bocas who kindly gave logistical support. Permits to collect were provided by three Panamanian ministries; Ministerio de Comercio e Industria (MICI), MiAmbiente, and El Ministerio de Cultura de Panamá (formerly Instituto Nacional de Cultura, INAC). We thank the Dirección Nacional del Patrimonio Histórico, Instituto Nacional de Cultura, Republica de Panamá for issuing Resolución 153‐14, permitting the excavation of units 60 and 61 at Sitio Drago and the Serracín family for access to the site – especially Juany and Willy Serracín and Ana Serracín de Shaffer. We also thank Daniel Schussheim for machining the shell smasher, the NYU Langone Genome Technology Center for sequencing our libraries, and Christina Bergey, Kathleen Grogan, and the other members of the Perry Lab for their discussion and analytical advice. Components of this work were supported by the National Science Foundation Graduate Research Fellowship program (DGE‐1255832, to A.P.S.), a grant from the National Science Foundation (BCS‐1554834 to G.H.P.), the Smithsonian Tropical Research Institute Short‐Term Fellowship Program (to A.P.S.), and the SNI program from the , Panamá (to A.O.). Secretaría Nacional de Ciencia y Tecnología e Innovación
Publisher Copyright:
© 2021 John Wiley & Sons Ltd
PY - 2021/7
Y1 - 2021/7
N2 - Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n = 3), Late Holocene (984–1258 before present [BP]) archaeological midden (n = 5), and mid-Holocene (5711–7187 BP) paleontological fossil coral reef (n = 5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n = 5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7× higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behaviour on mollusc evolutionary biology.
AB - Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n = 3), Late Holocene (984–1258 before present [BP]) archaeological midden (n = 5), and mid-Holocene (5711–7187 BP) paleontological fossil coral reef (n = 5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n = 5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7× higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behaviour on mollusc evolutionary biology.
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U2 - 10.1111/1755-0998.13361
DO - 10.1111/1755-0998.13361
M3 - Article
C2 - 33595921
AN - SCOPUS:85103202443
SN - 1755-098X
VL - 21
SP - 1517
EP - 1528
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
IS - 5
ER -