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Mitchell KJ, Rawlence NJ. Examining Natural History through the Lens of Palaeogenomics. Trends Ecol Evol 2021; 36:258-267. [PMID: 33455740 DOI: 10.1016/j.tree.2020.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.
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Affiliation(s)
- Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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Psonis N, de Carvalho CN, Figueiredo S, Tabakaki E, Vassou D, Poulakakis N, Kafetzopoulos D. Molecular identification and geographic origin of a post-Medieval elephant finding from southwestern Portugal using high-throughput sequencing. Sci Rep 2020; 10:19252. [PMID: 33159124 PMCID: PMC7648095 DOI: 10.1038/s41598-020-75323-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/06/2020] [Indexed: 02/02/2023] Open
Abstract
Molecular species identification plays a crucial role in archaeology and palaeontology, especially when diagnostic morphological characters are unavailable. Molecular markers have been used in forensic science to trace the geographic origin of wildlife products, such as ivory. So far, only a few studies have applied genetic methods to both identify the species and circumscribe the provenance of historic wildlife trade material. Here, by combining ancient DNA methods and genome skimming on a historical elephantid tooth found in southwestern Portugal, we aimed to identify its species, infer its placement in the elephantid phylogenetic tree, and triangulate its geographic origin. According to our results the specimen dates back to the eighteenth century CE and belongs to a female African forest elephant (non-hybrid Loxodonta cyclotis individual) geographically originated from west—west-central Africa, from areas where one of the four major mitochondrial clades of L. cyclotis is distributed. Historical evidence supports our inference, pointing out that the tooth should be considered as post-Medieval raw ivory trade material between West Africa and Portugal. Our study provides a comprehensive approach to study historical products and artefacts using archaeogenetics and contributes towards enlightening cultural and biological historical aspects of ivory trade in western Europe.
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Affiliation(s)
- Nikolaos Psonis
- Foundation for Research and Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology, Ancient DNA Lab, N. Plastira 100, Vassilika Vouton, 70013, Irakleio, Greece.
| | - Carlos Neto de Carvalho
- Naturtejo UNESCO Global Geopark-Geology Office of the Municipality of Idanha-a-Nova, Centro Cultural Raiano, Av. Joaquim Morão, 6060-101, Idanha-a-Nova, Portugal.,Instituto D. Luiz-IDL Ciências da Terra, Faculty of Sciences of the University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal
| | - Silvério Figueiredo
- Polytechnic Institute of Tomar, Quinta do Contador, Estrada da Serra, 2300-313, Tomar, Portugal.,Portuguese Center of Geo-History and Prehistory, Largo de São Caetano, 2150-265, Golegã, Portugal.,Geosciences Center-University of Coimbra, Rua Sílvio Lima, University of Coimbra, 3030-790, Coimbra, Portugal
| | - Eugenia Tabakaki
- Foundation for Research and Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology, Ancient DNA Lab, N. Plastira 100, Vassilika Vouton, 70013, Irakleio, Greece
| | - Despoina Vassou
- Foundation for Research and Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology, Ancient DNA Lab, N. Plastira 100, Vassilika Vouton, 70013, Irakleio, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, 71409, Irakleio, Greece.,Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, 70013, Irakleio, Greece
| | - Dimitris Kafetzopoulos
- Foundation for Research and Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology, Ancient DNA Lab, N. Plastira 100, Vassilika Vouton, 70013, Irakleio, Greece
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