Periodic Reporting for period 1 - STAMPEDE (Spatial and Temporal Analysis of Modern and Past Elephant DivErsity)
Reporting period: 2021-06-01 to 2023-05-31
Elephants played a prominent role in human history since the the ancient times, which is documented by an abundance of ivory products nowadays housed in public and private collections worldwide. Elephant ivory is an integral part of human history because it was a global commodity creating some of the oldest trade routes. Yet, very little is known about elephants in the historical times, because DNA and samples do not get preserved well in the hot climate of the low latitudes. However, an unexpected solution to the problem might be to study the ivory that has made its way out of Africa, and in this proof-of-concept project, I study three samples of ivory found in a shipwreck in the Mediterranean Sea. The ship, likely sailing from North Africa, sank 2,500 years ago near the coast of Spain. Understanding where did the ivory come from can provide information about genetic variation, and perhaps whole populations, which have become extinct since those times. To put these ancient samples in context, I first generate a genomic catalogue of present-day elephant diversity by sequencing whole genomes from elephants from across their current range. Besides being a genetic map, upon which the ancient samples can be projected, this dataset is also an invaluable resource for further elephant research and conservation. Thus, the overall objective of this project was to study the genetic diversity of African elephants that remains in the present, and to put it into the perspective of the diversity that has already gone extinct by studying ivory from a shipwreck.
In this project, I generated whole genomes for 227 African elephants, including both species currently living in Africa - the savanna elephant and the forest elephant. The elephants were sampled across 28 locations in 16 African countries, and thus they represent most of the present-day range of African elephants. The genomes generated in this project are of a very high quality - with each of the more than 3 billion letters of the elephant's genetic code covered on average 37-times. The sequencing was performed at the GeoGenetics Sequencing Center at the University of Copenhagen, the Roy J. Carver Biotechnology Center at the University of Illinois, and at Illumina, Inc. I downloaded more than 50 TB of data to the computational servers at the University of Copenhagen and mapped the raw sequencing data to the African savanna elephant and the Asian elephant reference genomes. This data was used for subsequent analyses of population structure, genetic diversity and inbreeding. However, it also serves as a reference dataset for projecting three samples of shipwreck ivory of unknown origin. From the three shipwreck samples, ancient DNA was extracted in a dedicated clean laboratory at the Globe Institute and was prepared for sequencing in the Center for Palaeogenetics in Stockholm. Sequencing revealed that the quality of these samples was very low, as the best of the three samples had ~0,3% authentic elephant DNA, with the rest originating from contamination. The low quality was confirmed with radiocarbon-dating, which failed to estimated the age of these samples due to low carbon content. Despite the challenges, analyses developed for low-depth samples revealed that one of the ivory pieces originates from a savanna elephant and likely somewhere at the northern edge of its range. Publications are currently being prepared to share these findings with the scientific community.
The outcomes of this project have impact on several scientific disciplines from conservation genetics to archaeology, but they also provides resources for improved conservation of two species threatened by extinction, and more broadly, inform us about an important chapter of human history. The modern genomes represent the largest genomic dataset current available for African elephants, increasing the number of available genomes ten-fold. These genomes provides answers about some of the outstanding questions in elephant research, but they are also a resource that can be exploited for direct conservation application. There is already a follow-up initiative to use this data to develop genetic tools for more effective monitoring of elephant populations. In addition, the ancient elephant DNA from 2,500-year-old shipwreck pushes the boundaries of studying elephants far back in time and offers a window to the past. Besides informing on the origin of this ivory, the outcomes represent a proof-of-concept experiment showing that elephants can be studied on historical time scales, which opens up a new avenue of research on the border between natural and historical sciences.