Molecular identification and geographic origin of a post-Medieval elephant finding from southwestern Portugal using high-throughput sequencing

Nikolaos Psonis,Nikos Poulakakis,Despoina Vassou,Eugenia Tabakaki,Dimitris Kafetzopoulos,Silvério Figueiredo,Carlos Neto De Carvalho

doi:10.1038/s41598-020-75323-y

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.

Highlights

Molecular species identification plays a crucial role in archaeology and palaeontology, especially when diagnostic morphological characters are unavailable
When using the entire genomes of the two African elephant species in a FastQ Screen analysis, in order to investigate if the tooth belongs to a “pure” forest elephant or to a hybrid, the results showed a much higher percentage of total reads being mapped to L. cyclotis than to L. africana, whereas the same was observed when accounting the uniquely mapped reads to one genome only
We performed archaeogenetic genome skimming analysis in a molar tooth found in the southwestern Portuguese coast in order to identify the species and determine its geographic origin

Summary

Introduction

Molecular species identification plays a crucial role in archaeology and palaeontology, especially when diagnostic morphological characters are unavailable. We combine ancient DNA methods and genome skimming on a historic elephantid molar tooth found in the southwestern Portugal coast, in order to identify the species that belongs, and narrow down its geographic origin To achieve this goal, we performed molecular species identification using a competitive mapping, as well as a metagenomics approach, whereas the sample’s providence was circumscribed through the phylogenetic placement of its mitochondrial DNA consensus sequence into the phylogenetic tree of extant elephants containing the majority of discrete clades and subclades discovered over the last two d ecades[13]. Taking into account these results, the present study attempts to enlighten some cultural and biological historical aspects of ivory in west Europe, relating to the trading networks, market and consuming of products and artefacts

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Conclusion