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

Lead Research Organisation: University of Oxford
Department Name: Museum of Natural History

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 een 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 answers questions such as, with which archaic human lineages (e.g. Neanderthals, Denisovans, H. erectus, H. antecessor) the modern human lineage (us) had physical contact 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
 
Title Denny Lice Collection - Photography of collection specimens 
Description High resolution photographs of all specimens and related labels completed. Files stored as .TIFF and .PNG for different uses. Not shared outside of project at large yet, however some images have been used for outreach and engagement purposes. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact The images, plus meta data on the Denny collection will be made available via the Museum's "collections on-line" portal which is currently being developed for released late 2018 or early 2019. The Denny collection on-line will enable researchers to access high resolution images and all associated meta data concerning the Denny Lice Collection 
 
Title Denny Lice Collection - Specimen level database 
Description Database completed of 600 lots of specimens, including all data provided in labels for easy access and reading. Data includes host species names (and latin names added in where absent), location specimen collected, collector, date of collection, number of specimens per lot, other notes included. Not yet shared online, but this is in the pipeline for future engagement with the collection when fully curated. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact The images, plus meta data on the Denny collection will be made available via the Museum's "collections on-line" portal which is currently being developed for released late 2018 or early 2019. The Denny collection on-line will enable researchers to access high resolution images and all associated meta data concerning the Denny Lice Collection 
 
Title Denny archive digital database and transcription 
Description The archive of written material in the collection was scanned at high resolution in order to digitally preserve this delicate resource. The archive included lists of specimens in the collection and an incomplete manuscript of Denny's documenting the Exotic Anoplura of the world. All text has been transcribed into digital format to allow easy access for study and cross-referencing with the physical collection. A number of copper plates and their prints were also scanned. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact The Denny archive and transcripts will be made available on-line, this will enable researchers interested in live ecology, biology and taxonomy access this information which is currently unavailable. 
 
Title Excel database of Henry Denny publications and species (future publication) 
Description Database completed of all papers, letters and notes published by Henry Denny during his lifetime. Also including all of the species of lice Denny officially described and their locations where known. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Not yet shared but the information will be published in a biography of Henry Denny in the future to increase knowledge of his extensive work to the wider world. 
 
Description "Super Science Saturday" - Oxford University Museum of Natural History Science Fair 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Large public event at Oxford University Museum (total visitors - 3,500+ people) presenting the project and research at the museum to the public. Stall included microscope viewing of lice, learning about keys for identification, 3D prints of Denny Lice for object handling and learning about lice morphology, and information sheets.
Aimed at a family audience but questions also ranged to academic laypeople interested in the wider project.
Resulted in engagement with the project and interest in all aspects of the research.
Photos available.
Year(s) Of Engagement Activity 2018
URL http://www.ox.ac.uk/event/super-science-saturday-1
 
Description Half Term activity 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Halloween themed activity table looking at lice under microscopes and learning about the group.
Aimed at young children and families visiting the museum during school half term.
Result was lots of interest and questions about lice from the children, and the wider project from adults visiting.
October 2017.
Photos available
Year(s) Of Engagement Activity 2017
 
Description Photography MSc Project Spotlight  
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact MSc student from Nottingham University visited the collection and archive to spotlight in their final thesis project towards an MSc in Biological Photography & Imaging, with a view to enter it into an exhibition after the completion of the project.
Year(s) Of Engagement Activity 2017
 
Description Spotlight Specimens 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact A 30 minute slot every month in the OUMNH main court, during which specimens are on display and the public can ask and learn about lice and genetics.
Reach is local, members of the public currently in the museum at the time of the spotlight, although during busy times many international visitors may also be present.
Audience is the public with layman's knowledge of science. The activity is adjusted based on age so all participants can leave with more scientific knowledge than they arrived with.
Images available
Year(s) Of Engagement Activity 2017,2018
 
Description Super Science Saturday 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Large event at OUMNH presenting the project and research at the museum to the public. Stall included microscope viewing of lice, learning about keys for identification, 3D prints for learning about morphology, and information sheets.
Aimed at a family audience but questions also ranged to academic laypeople interested in the wider project.
Resulted in engagement with the project and interest in all aspects of the research.
Photos available.
Year(s) Of Engagement Activity 2018
 
Description Taxonomy Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact An activity developed for a taxonomy day for high school age students in the museum, consisting of the use of dichotomous keys to identify invertebrates and learning about lice taxonomy.
Audience High school students
Resulted in students gaining knowledge of a technique still used widely in science today, and getting more interested in some lesser known scientific jobs as career options.
September 2017.
Feedback available
Year(s) Of Engagement Activity 2017
 
Description Twitter takeover weeks 
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 Two weeks in the past 12 months during which project-related tweets are published every day Monday-Friday on the OUMNH twitter account. Tweets always accompanied by high resolution images and a hashtag (#dennylice) for people to retweet and search.
Reach is global based on the OUMNH twitter audience, tweets were aimed at science-interested laypeople and any questions posed were answered promptly for continuing engagement.
Impact of this style of outreach means members of the public can interact and learn about lice and entomology, as well as the project, without needing to be physically present in the museum.
August 2017 and January 2018
Year(s) Of Engagement Activity 2017,2018
URL https://twitter.com/morethanadodo?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor
 
Description Wildfair Pop-up Scientist 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Two thirty minute slots of project outreach to the public on a Saturday family event day in OUMNH. Specimens on display to view.
The event was very busy with over 100 members of the public visiting the stall over the two slots. All ages present so engagement tailored to this.
Impact got people interested in entomology and the use of old collections with new methodologies.
June 2017
Photos available
Year(s) Of Engagement Activity 2017