Unravelling early human migration in southern South America using Darwin's Fuegian lice

Lead Research Organisation: University of Reading
Department Name: Sch of Biological Sciences

Abstract

Some 15,000 years ago, tribes entered America from Siberia to people the Americas. These tribes continued along the west coast of America until they reached the small islands of Tierra del Fuego in the far South. During his voyage on the Beagle, Charles Darwin obtained lice from two human groups, Fuegians and Chonos. These lice are different from modern lice and they still contain the blood of the Indians. These tribes went extinct soon after Darwin's visit. Lice collected by Darwin, Wallace and others from extinct human tribes, extinct animals like the Tasmanian wolf and many more animals, total some 3000 specimens. They are currently in the Denny lice collection of the Natural History Museum, University of Oxford. However, there is no catalogue of these lice, not even the total number is known, and most specimens have never been identified. The specimens themselves are at the point of being lost forever. We propose to rescue and curate the Denny collection, to make these lice and the blood they carry inside (from extinct hosts) available to the scientific and public community. Using advanced ancient DNA methods that have been successful on a 400,000 year-old human bone, we propose to carry out genetic analyses on the 180 year-old Darwin lice and the human mitochondria of the blood meal inside these lice.
We have identified a modern, but remote and isolated Central American tribe currently carrying the head louse species Pediculus pseudohumanus and a South American tribe carrying a new species of lice with a different karyotype (number of chromosomes). P. pseudohumanus has also been described from Polynesian Indians and monkeys. By sequencing these two modern lice species and comparing them with the louse of chimpanzees and bonobos, P. schäffi, as well as with the results of the Fuegian and Chonos lice, we aim to trace human migration in South America and unravel whether lice jumped from primates to humans or vice-versa. Our pubic lice, for example, have likely been acquired by our ancestors from gorillas, hunted about 3-4 million years ago.
The lice that modern humans carry at present on their heads can be divided into three clades (genetic groups). Clade A is found in Africa and rest of the World, B in Europe, America and Australia, and C in Ethiopia, Senegal and Nepal. Using a single mitochondrial gene fragment, it has been estimated that the clade A and B lineages separated between 700,000 and 1.2 million years ago and that clade C split around 2 millions ago. These large range estimations are not helpful because they do not tell us from whom these lice came. Clade A and B lice, did they come from Neanderthals, from Denisovans, from Homo erectus, or from H. antecessor? The age estimation of clade C lice is so vague that we cannot even make a useful guess. The genome of clade A lice have already been sequenced. We propose to determine the genetic sequence of clade B and C lice to obtain a time estimate as precise as possible for the split of the lice lineages. While it would be interesting enough to unravel the phylogenomics of human lice, the importance lies in the fact that we carry all these lice, which proves that the modern human lineage had physical contact with these archaic humans, e.g. H. erectus.
Lice cannot survive for more than a few hours off their host, so archaic and modern human lineages or species had to overlap in time and space to physically exchange their lice. This physical contact to exchange living head lice is a unique feature. Evidence about contact with no interbreeding, and the time of contact cannot be retrieved from any human sequencing, ancient or modern, only from lice. This proposal aims to identify with which archaic human lineage or species we had physical contact in the past and when. Since at the moment we carry three different clades of lice on our heads, we must have had two separate encounters with other human lineages, separated by roughly one million years

Technical Summary

The Henry Denny Anoplura collection at Oxford University Museum of Natural History contains ~3,000 lice in 600 'lots'. Many of them were collected by Charles Darwin, Alfred Wallace and other contemporary entomologists. Lice from human hosts include those from extinct tribes, and from animals such as the Tasmanian wolf. Most of these specimens contain the last blood meal of their host. The collection remains untouched since its arrival in the Museum (1871), and only unpublished archival catalogues exist on its contents and value. The collection in its current state has little scientific value; we therefore propose to digitize, research the archives, re-curate specimens, identify/image each species, aiming to make the collection available on-line to the public and scientific community.

We propose to sequence the DNA of the lice and the mtDNA of the blood meal collected from Chonos and from Haush (Fuegians). We developed a feasibility test that guarantees good yielding of DNA from both lice and host-blood. Assuming a worst-case scenario of only 0.1 % endogenous DNA, we propose extraction of DNA with a silica-capture method for DNA shorter than 40 bp and build Gansauge & Meyer single-strand DNA libraries. We aim at sequencing all extant lice genomes at 20 x coverage with 125 PE, extinct lice genomes at 4 x coverage with 75 PE, and extinct human mitochondria at 40 x coverage 75 PE, all on HiSeq 2500. The sequencing results will be used to answer hypothesis about the peopling of South America, eg, the contribution of Polynesians, to investigate the transfer of lice from humans to primates and primates to humans, and to date precisely the split of clade A, B and C lice in order to determine the identity and time of the two exchanges of head lice between the modern human lineage and two archaic human lineages or species.

Planned Impact

This proposal will contribute to the nation's culture. It will for the first time celebrate the unique Anoplura Exotica and Britannica collection created by the foremost louse authority of his day Mr Henry Denny (1803-1871). It will research, restore, curate, digitise and make available lice collected by famous scientists such as Charles Darwin and Alfred Russel Wallace to the research community and wider public through an on-line presence. It will enable research related to extinct human tribes and extinct animal species. It will enhance public knowledge and understanding of the importance of taxonomy and museum collections in current research. It proposes to answer questions such as, with which archaic human lineages (e.g. Neanderthals, Denisovans, H. erectus, H. antecessor) the modern human lineage (us) had physical contact with to obtain its head lice? Recent publications, for example, on the discovery of 400,000 year-old Denisovan bones in Spain have through the analysis of ancient DNA sequencing had a huge impact, both scientifically and through the popular media. The proposed work investigating human interaction and migration through analysis of ancient and modern head lice is likely to generate similar impact.
A travelling exhibition and associated lectures will be targeted at multiple levels: school, the general public and undergraduate/postgraduate students. This will enable knowledge exchange across a range of audiences at multiple venues. The project will also feature as part of the Oxford Museums' 'Investigators' project, a 10 week research project aimed at 14-16 year old students as part of the British Science Association CREST award. In addition the Museum will offer opportunities for students in the first year of a post-16 science, technology, engineering and maths (STEM) course to participate in the project as part of the Nuffield Research Placement scheme.
The proposed work on applying ancient DNA sequencing techniques on human blood inside human lice has direct impact on forensic trace analysis. It will directly benefit the commercial forensic sector by expanding their analytical capabilities and it will benefit the public sector in the form of the public prosecution by facilitating reviews of cold cases that so far have been considered too old for trace analysis.
Research staff will gain skills in various areas that currently show a shortage in the labour market. The restoration and curation work comes with skills in alpha taxonomy, a priority area according to the House of Lords report. Practical and bioinformatic skills in next generation sequencing of ancient DNA traces and whole genome analyses are thought after in many new and expanding biotechnology companies.

Publications

10 25 50
 
Description We were able to demonstrate that human lice and their nits/eggs can provide genetic information of their ancient human hosts; preventing the destruction of unique and valuable human specimens, preventing the destruction of well preserved skeletons or mummies.
The DNA provided by lice allowed for the 1st time to unravel unknown ancient migratory routes in southern South America, see 10.1093/molbev/msab351
The DNA off ancient lice allowed us the find for the 1st time Merkel cell polyomavirus, the oldest record from a mummy 2000 years old; we are now investigating if head lice can be vectors.
Using geometric morphometrics (the shape) of lice from historical collections, where DNA cannot longer be obtained we manage to extract information on lice host diversity and investigate human migrations and history.
Exploitation Route Very interesting results so far, leading to high impact publications, some of which are being written. The findings of the published 10.1093/molbev/msab351 being used in archaeology and Ancient DNA studies worldwide.
This opens us endless possibilities for the study of museum collections, for example hair samples and skins of animals
Sectors Education,Culture, Heritage, Museums and Collections

 
Description On one side, the project itself helps in the recovery, preservation and awareness of unique archaeological sites in America and rescuing cultural inheritance of indigenous people. On another side, this project facilitated involvement in investigations of mass graves as the result of armed conflicts, where the use non-human biological trace evidence will be implemented I addition, it has increased the number of consultations over the use of human lice to unravel crime cases (ongoing case work). The police from several countries including UK has or is consulting the PIs.
First Year Of Impact 2017
Sector Communities and Social Services/Policy,Education,Environment,Government, Democracy and Justice,Culture, Heritage, Museums and Collections,Security and Diplomacy
Impact Types Cultural,Societal

 
Description Educational, mobile exhibition presenting the value of ancient collections (Museo de Tierra del Fuego)
Geographic Reach South America 
Policy Influence Type Influenced training of practitioners or researchers
Impact Provided evidence of the value of archaeological sites in Tierra del Fuego, helping indigenous people rescue their history and cultural values.
 
Description Engagement with Indigenous communities in South America, for research on ancient migrations and cultures
Geographic Reach National 
Policy Influence Type Contribution to new or Improved professional practice
Impact A new method to obtain information of the original inhabitants of South America (through their parasites, lice) educates: i)museum curators on the preservation of ancient specimens; ii)educates Indigenous Peoples on how they can study their history without having to destroy their ancient remains; iii) instruct the researchers, skilled workforce on new ways to approach Indigenous Peoples to study human history.
 
Description Study of mass graves, forensic work related to this grant
Geographic Reach National 
Policy Influence Type Contribution to new or Improved professional practice
 
Description Cesar Milstein Travel award
Amount $ 330,000 (ARS)
Organisation Argentinean National Agency for Science and Technology 
Sector Public
Country Argentina
Start  
 
Description Indian Government bursary
Amount £100,000 (GBP)
Organisation Government of India 
Sector Public
Country India
Start 09/2017 
End 09/2021
 
Description SYNTHESYS
Amount € 1,200 (EUR)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 05/2016 
End 07/2016
 
Description University of Costa Rica
Amount £1,000 (GBP)
Organisation University of Costa Rica 
Sector Academic/University
Country Costa Rica
Start 08/2018 
End 11/2018
 
Title DNA extraction of human DNA from ectoparasites 
Description In development, so far tests are promising and we can extract high quality DNA from e.g. nit remains; therefore there is no need to use bones or teeth, no destructive sampling 
Type Of Material Biological samples 
Year Produced 2017 
Provided To Others? No  
Impact No more need to access to sensitive material such as bodies/remain of indigenous people; great impact on society 
 
Title Host DNA is protected by the cement that glues head lice nits to the hair of ancient mummies. Ancient lice morphology help gather information on ancient environmental parameters before the death of the hosts 
Description Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500-2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history. 
Type Of Material Biological samples 
Year Produced 2021 
Provided To Others? Yes  
Impact Initially to professionals working on ancient DNA; for Holocene samples from archaeological sites the methods provide new means, non-destructive sampling methods to study human history and evolution throughout their lice. Lice themselves, their position and state on the scalp provide information of the environment in which their hosts were living 
URL http://doi.org/10.1093/molbev/msab351
 
Title European Nucleotide Archive under the accession number PRJEB49684 
Description Ancient human lice and host DNA from ancient samples of lice and humans from Argentina and Borneo; mtDNA and full genomes 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact A new method of obtaining ancient human (host) DNA and valuable information of the life of these ancient hosts from their lice 
URL https://www.ebi.ac.uk/ena/browser/text-search?query=PRJEB49684
 
Description Chimpanzee/Bonobo collaboration with Barcelona 
Organisation Pompeu Fabra University
Country Spain 
Sector Academic/University 
PI Contribution Sequencing from traces; interpretation of results
Collaborator Contribution Bioinformatics and interpretation of results
Impact Not yet
Start Year 2019
 
Description Collaboration with Argentinean Museum, Dr. Teresa Michielli 
Organisation Mariano Gambier Museum
Country Argentina 
Sector Private 
PI Contribution Knowledge on lice infestations in prehispanic civilisations
Collaborator Contribution Provision of lice infestations, on the mummies heads
Impact Not yet
Start Year 2016
 
Description Collaboration with Congo, bonobo lice 
Organisation Lola ya Bonobo
Country Congo, the Democratic Republic of the 
Sector Charity/Non Profit 
PI Contribution N/A yet. I have proposed a project in collaboration
Collaborator Contribution N/A yet
Impact Not yet
Start Year 2018
 
Description Historical collections of insects 
Organisation University of Hamburg
Department Center of Natural History (CeNak)
Country Germany 
Sector Academic/University 
PI Contribution Identification of ectoparasites of apes
Collaborator Contribution Historical collection specimens
Impact Not yet
Start Year 2020
 
Description International Collaborative Agreement with Prof. Teresa Michieli, San Juan, Argentina 
Organisation Mariano Gambier Museum
Country Argentina 
Sector Private 
PI Contribution N/A yet
Collaborator Contribution Samples from mummies, over 34 samples
Impact Memorandum of Understanding: "Estudio evolutivo y de interacción ambiental de material arqueológico: piojos y sus portadores, de la colección del Instituto de Investigaciones Arqueológicas y Museo Prof. Mariano Gambier"
Start Year 2017
 
Description International collaboration with Museo de arte precolombino, Santiago de Chile 
Organisation Chilean Museum of Pre-Columbian Art
Country Chile 
Sector Charity/Non Profit 
PI Contribution N/A yet
Collaborator Contribution Samples from ca 15 mummies and artefacts
Impact N/A yet
Start Year 2017
 
Description 10+ Interviews for international news/outlets including The Smithsonian magazine, The Scientist, BBC World, INFOBAE, El Espectador, The Guardian, The NYT, The Independent, etc 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Initial interviews with international outlets generated a chain of new interviews all over the world as the the new method and the new findings on early human migrations is of great impact on culture
Year(s) Of Engagement Activity 2021,2022
URL https://www.the-scientist.com/news-opinion/scratchy-scalps-help-glue-together-pieces-of-an-ancient-p...
 
Description International press release 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This news outlet reaches professionals and the public sector for topics with great impact to the general public and also to the development of scientific research, new methods. In this case it was the discovery of a new source of high quality ancient DNA, that is the DNA trapped in the cement of louse nits, ancient nits. By using a handful of ancient nits there is no need to break the skull of a valuable specimen, a mummy or well preserved skeleton, as the ancient DNA of the host is found in nits. The DNA from the nits indicated the presence, in the oldest individual, of a virus that produces skin cancer; the oldest record of this virus so far. Morphological analyses of lice and nits from ancient specimens also provided information of the environmental conditions where these ancient peoples were living and died, suggesting the cause of death.
Year(s) Of Engagement Activity 2022
URL https://www.the-scientist.com/news-opinion/scratchy-scalps-help-glue-together-pieces-of-an-ancient-p...
 
Description International press release 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This news outlet reaches professionals and the public sector for topics with great impact to the general public and also to the development of scientific research, new methods. In this case it was the discovery of a new source of high quality ancient DNA, that is the DNA trapped in the cement of louse nits, ancient nits. By using a handful of ancient nits there is no need to break the skull of a valuable specimen, a mummy or well preserved skeleton, as the ancient DNA of the host is found in nits. The DNA from the nits indicated the presence, in the oldest individual, of a virus that produces skin cancer; the oldest record of this virus so far. Morphological analyses of lice and nits from ancient specimens also provided information of the environmental conditions where these ancient peoples were living and died, suggesting the cause of death.
Year(s) Of Engagement Activity 2022
URL https://scienmag.com/nits-on-ancient-mummies-shed-light-on-south-american-ancestry/
 
Description International press release 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This news outlet reaches professionals and the public sector for topics with great impact to the general public and also to the development of scientific research, new methods. In this case it was the discovery of a new source of high quality ancient DNA, that is the DNA trapped in the cement of louse nits, ancient nits. By using a handful of ancient nits there is no need to break the skull of a valuable specimen, a mummy or well preserved skeleton, as the ancient DNA of the host is found in nits. The DNA from the nits indicated the presence, in the oldest individual, of a virus that produces skin cancer; the oldest record of this virus so far. Morphological analyses of lice and nits from ancient specimens also provided information of the environmental conditions where these ancient peoples were living and died, suggesting the cause of death.
Year(s) Of Engagement Activity 2022
URL https://www.bbc.com/mundo/noticias-59873097
 
Description International press release 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This news outlet reaches professionals and the public sector for topics with great impact to the general public and also to the development of scientific research, new methods. In this case it was the discovery of a new source of high quality ancient DNA, that is the DNA trapped in the cement of louse nits, ancient nits. By using a handful of ancient nits there is no need to break the skull of a valuable specimen, a mummy or well preserved skeleton, as the ancient DNA of the host is found in nits. The DNA from the nits indicated the presence, in the oldest individual, of a virus that produces skin cancer; the oldest record of this virus so far. Morphological analyses of lice and nits from ancient specimens also provided information of the environmental conditions where these ancient peoples were living and died, suggesting the cause of death.
Year(s) Of Engagement Activity 2022
URL https://www.sciencedaily.com/releases/2021/12/211228220818.htm
 
Description International press release, Europe 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This news outlet reaches professionals and the public sector for topics with great impact to the general public and also to the development of scientific research, new methods. In this case it was the discovery of a new source of high quality ancient DNA, that is the DNA trapped in the cement of louse nits, ancient nits. By using a handful of ancient nits there is no need to break the skull of a valuable specimen, a mummy or well preserved skeleton, as the ancient DNA of the host is found in nits. The DNA from the nits indicated the presence, in the oldest individual, of a virus that produces skin cancer; the oldest record of this virus so far. Morphological analyses of lice and nits from ancient specimens also provided information of the environmental conditions where these ancient peoples were living and died, suggesting the cause of death.
Year(s) Of Engagement Activity 2022
URL https://www.europapress.es/ciencia/ruinas-y-fosiles/noticia-liendres-momias-arrojan-luz-migraciones-...
 
Description International press release, the whole of Latin America 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This news outlet reaches professionals and the public sector for topics with great impact to the general public and also to the development of scientific research, new methods. In this case it was the discovery of a new source of high quality ancient DNA, that is the DNA trapped in the cement of louse nits, ancient nits. By using a handful of ancient nits there is no need to break the skull of a valuable specimen, a mummy or well preserved skeleton, as the ancient DNA of the host is found in nits. The DNA from the nits indicated the presence, in the oldest individual, of a virus that produces skin cancer; the oldest record of this virus so far. Morphological analyses of lice and nits from ancient specimens also provided information of the environmental conditions where these ancient peoples were living and died, suggesting the cause of death.
Year(s) Of Engagement Activity 2022
URL https://www.infobae.com/america/ciencia-america/2021/12/28/descubren-los-origenes-de-momias-de-san-j...
 
Description Interviews and work on documentaries and podcasts on trace evidence analysis (non-human) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Short documentary in preparation for the BBC on how small arthropods help unravel circumstances around a crime; A short film in SpunGold TV, featuring a cold case and the analysis of arthropod evidence.
Year(s) Of Engagement Activity 2018,2019,2021
 
Description Prominent on international news 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This news outlet reaches professionals and the public sector for topics with great impact to the general public and also to the development of scientific research, new methods. In this case it was the discovery of a new source of high quality ancient DNA, that is the DNA trapped in the cement of louse nits, ancient nits. By using a handful of ancient nits there is no need to break the skull of a valuable specimen, a mummy or well preserved skeleton, as the ancient DNA of the host is found in nits. The DNA from the nits indicated the presence, in the oldest individual, of a virus that produces skin cancer; the oldest record of this virus so far. Morphological analyses of lice and nits from ancient specimens also provided information of the environmental conditions where these ancient peoples were living and died, suggesting the cause of death.
Year(s) Of Engagement Activity 2022
URL https://www.smithsonianmag.com/science-nature/mummies-secrets-revealed-by-ancient-dna-preserved-in-l...
 
Description Scientific visit, interview and mobile exhibition 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview published in the museum. Work in the Museum and delivery of mobile exhibition
Year(s) Of Engagement Activity 2018
URL https://mfm.tierradelfuego.gov.ar/un-acercamiento-al-adn-de-los-pueblos-originarios-a-traves-de-pioj...
 
Description Scientific visit, sampling. Interview and mobile exhibition for Museo Chilean de Arte Precolombino 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview released in the website of the Museo Chilean de Arte Precolombino

Mobile exhibition about studies of lice from Fuegian and Chonos, collected by Charles Darwin, delivered and presented in the Museum (2 posters with specimens)
Year(s) Of Engagement Activity 2017,2018
URL http://www.precolombino.cl/museo/noticias/la-voz-de-los-piojos/
 
Description Visiting and working in museums abroad 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Working with anthropologists and archaeologists on museum collections in Europe and in South America.
The most influential is the visit and access to the lice of mummies in the Museum Mariano Gambier, dating around 6000 years.

We are working with the anthropologist Dr. Teresa Michielli a manuscript on the level of infestation found on these mummies.
Year(s) Of Engagement Activity 2016
URL http://wwwmuseogambiericp.blogspot.co.uk