Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama
| Autor: | Stephanie Marciniak, George H. Perry, Thomas A. Wake, Aaron O'Dea, Alexis P. Sullivan |
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| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
0301 basic medicine Mitochondrial DNA Strombus pugilis Panama Gastropoda 010603 evolutionary biology 01 natural sciences Conch Evolution Molecular 03 medical and health sciences Genetics Animals Humans DNA Ancient Ecology Evolution Behavior and Systematics Holocene Cell Nucleus geography geography.geographical_feature_category biology Land snail Chromosome Mapping Coral reef DNA Sequence Analysis DNA biology.organism_classification Archaeology Midden 030104 developmental biology Ancient DNA Caribbean Region Genome Mitochondrial Biotechnology |
| Zdroj: | Molecular ecology resourcesREFERENCES. 21(5) |
| ISSN: | 1755-0998 5711-7187 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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