Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes
- University of Copenhagen, Denmark
- Universidad de Chile, Chile
- Universidad Católica del Norte, Chile
- Austral University of Chile, Chile
- University of Chile, Chile
- University of Porto, Portugal
- Cardiff University, United Kingdom
- Bio-Bio University, Chile
Abstract
The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en-masse. In this study we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 - 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.
Data availability
Sequencing data have been deposited in GenBank under accession codes:BankIt2325854 C10mito MT254135BankIt2325854 C11mito MT254136BankIt2325854 C12mito MT254137BankIt2325854 c13mito MT254138BankIt2325854 C14mito MT254139BankIt2325854 C15mito MT254140BankIt2325854 C16mito MT254141BankIt2325854 C18mito MT254142BankIt2325854 c1mito MT254143BankIt2325854 C20mito MT254144BankIt2325854 C21mito MT254145BankIt2325854 C22mito MT254146BankIt2325854 C24mito MT254147BankIt2325854 C25mito MT254148BankIt2325854 C27mito MT254149BankIt2325854 C28mito MT254150BankIt2325854 C29mito MT254151BankIt2325854 C30mito MT254152BankIt2325854 C31mito MT254153BankIt2325854 C32mito MT254154BankIt2325854 C33mito MT254155BankIt2325854 C34mito MT254156BankIt2325854 C35mito MT254157BankIt2325854 C36mito MT254158BankIt2325854 C37mito MT254159BankIt2325854 C38mito MT254160BankIt2325854 C39mito MT254161BankIt2325854 C41mito MT254162BankIt2325854 C42mito MT254163BankIt2325854 C43mito MT254164BankIt2325854 C44mito MT254165BankIt2325854 C46mito MT254166BankIt2325854 C47mito MT254167BankIt2325854 C48mito MT254168BankIt2325854 C49mito MT254169BankIt2325854 C50mito MT254170BankIt2325854 C52mito MT254171BankIt2325854 C54mito MT254172BankIt2325854 C55mito MT254173BankIt2325854 C57mito MT254174BankIt2325854 C59mito MT254175BankIt2325854 C5mito MT254176BankIt2325854 C60mito MT254177BankIt2325854 C61mito MT254178BankIt2325854 C62mito MT254179BankIt2325854 C63mito MT254180BankIt2325854 C64mito MT254181BankIt2325854 C65mito MT254182BankIt2325854 C66mito MT254183BankIt2325854 C67mito MT254184BankIt2325854 C68mito MT254185BankIt2325854 C69mito MT254186BankIt2325854 C6mito MT254187BankIt2325854 C70mito MT254188BankIt2325854 C71mito MT254189BankIt2325854 C72mito MT254190BankIt2325854 C73mito MT254191BankIt2325854 C74mito MT254192BankIt2325854 C75mito MT254193BankIt2325854 C76mito MT254194BankIt2325854 C77mito MT254195
Article and author information
Author details
Paloma Fernández Diaz-Maroto
Funding
Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica (1070040)
- Paloma Fernández Diaz-Maroto
Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica (1020316)
- Paloma Fernández Diaz-Maroto
Fondo Nacional de Desarrollo Científico y Tecnológico (1130917)
- Paloma Fernández Diaz-Maroto
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Diaz-Maroto et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 7,802
- views
-
- 551
- downloads
-
- 21
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes
eLife 10:e63390.
https://doi.org/10.7554/eLife.63390
Further reading
-
- Epidemiology and Global Health
- Evolutionary Biology
Several coronaviruses infect humans, with three, including the SARS-CoV2, causing diseases. While coronaviruses are especially prone to induce pandemics, we know little about their evolutionary history, host-to-host transmissions, and biogeography. One of the difficulties lies in dating the origination of the family, a particularly challenging task for RNA viruses in general. Previous cophylogenetic tests of virus-host associations, including in the Coronaviridae family, have suggested a virus-host codiversification history stretching many millions of years. Here, we establish a framework for robustly testing scenarios of ancient origination and codiversification versus recent origination and diversification by host switches. Applied to coronaviruses and their mammalian hosts, our results support a scenario of recent origination of coronaviruses in bats and diversification by host switches, with preferential host switches within mammalian orders. Hotspots of coronavirus diversity, concentrated in East Asia and Europe, are consistent with this scenario of relatively recent origination and localized host switches. Spillovers from bats to other species are rare, but have the highest probability to be towards humans than to any other mammal species, implicating humans as the evolutionary intermediate host. The high host-switching rates within orders, as well as between humans, domesticated mammals, and non-flying wild mammals, indicates the potential for rapid additional spreading of coronaviruses across the world. Our results suggest that the evolutionary history of extant mammalian coronaviruses is recent, and that cases of long-term virus–host codiversification have been largely over-estimated.
-
- Evolutionary Biology
Haldane’s rule occupies a special place in biology as one of the few ‘rules’ of speciation, with empirical support from hundreds of species. And yet, its classic purview is restricted taxonomically to the subset of organisms with heteromorphic sex chromosomes. I propose explicit acknowledgement of generalized hypotheses about Haldane’s rule that frame sex bias in hybrid dysfunction broadly and irrespective of the sexual system. The consensus view of classic Haldane’s rule holds that sex-biased hybrid dysfunction across taxa is a composite phenomenon that requires explanations from multiple causes. Testing of the multiple alternative hypotheses for Haldane’s rule is, in many cases, applicable to taxa with homomorphic sex chromosomes, environmental sex determination, haplodiploidy, and hermaphroditism. Integration of a variety of biological phenomena about hybrids across diverse sexual systems, beyond classic Haldane’s rule, will help to derive a more general understanding of the contributing forces and mechanisms that lead to predictable sex biases in evolutionary divergence and speciation.
