Twigstats software sheds light on mysteries of Europe's old-school migrators
- Reference: 1736074868
- News link: https://www.theregister.co.uk/2025/01/05/twigstats_genetic_analysis/
- Source link:
Speaking to The Register , mathematician and open source maintainer Leo Speidel said he hoped the project would go on to help reveal the human genetic history of Japan, Poland, and the UK.
Speidel, who recently started as group leader in interdisciplinary math and science at Japan's research institute RIKEN, was the first author of research, which sheds new light on population movements during the Roman occupation of Northern Europe, as well as Anglo-Saxon and Viking migration in the first millennium.
[2]
[3]Hitting the headlines , the study promises new evidence for a much-debated period of European history.
[4]
[5]
Speidel said the software project powering the study – dubbed Twigstats – is built on an earlier tool that has been widely used in the field since 2019 to help date genetic mutations and build a genetic family tree. Mutations cascade through genetic history, so the more mutations one individual shares with another, the more closely related they are to each other.
Coded in C++ and employing the statistical language R, Twigstats allows researchers to focus on a specific period in history with more fine-grained analysis than previously possible. Demand for such analysis has grown since researchers developed techniques for extracting DNA from ancient bones over the last 15 years (see Tom Higham's excellent book, [6]The World Before Us , for a description of these techniques). DNA from samples more than 100,000 – even a million – years old has been successfully extracted.
[7]
"We can now take these mutations, throw away old mutations, and focus on the more recent mutations," Speidel said. "Those more recent mutations should be more informative on events that happened quite recently. If you're interested in the first millennium AD in Europe, then you're interested in mutations that are closer to that time period than mutations that occurred hundreds of thousands of years ago. The idea was to take mutations, throw away the old ones, and focus on the more recent ones and that increases the signal-to-noise ratio manyfold and allows us to get a better sense of these mixtures."
[8]Tardigrade genes may hold secret to radiation treatments for humans
[9]Say hello to the epi-bit, a new approach to DNA data storage
[10]Heart of glass: Human genome stored for 'eternity' in 5D memory crystal
[11]In homage to Jurassic Park, researchers store DNA in amber-like polymer
The research published this week was led by the Francis Crick Institute, where Speidel was a postdoctoral researcher.
Pontus Skoglund, group leader of the Ancient Genomics Laboratory at the Crick and senior author, said: "The goal was a data analysis method that would provide a sharper lens for fine-scale genetic history. Questions that wouldn't have been possible to answer before are now within reach to us, so we now need to grow the record of ancient whole-genome sequences."
Speidel continues to maintain Twigstats, which is available as an open source project under the permissive MIT licence, and hopes other researchers will contribute.
He said other studies hoping to use the software are set to look into population movements in Anglo-Saxon England, Poland, and ancient Japan. But he said the technique could be equally applied to other species. "This isn't only applicable to humans; we can apply this to essentially any sort of sexually reproducing organism, like other mammals, and even plants and fish and all sorts of things," he said.
[12]
"What's really nice is that it's quite simple. It combines two ideas, starting off with mutations and these existing tests with ancient DNA will add. We were able to combine those two to make this new tool. The hope is that it's quite similar to what people are already doing and doesn't really need a big change in thinking from the user side." ®
Get our [13]Tech Resources
[1] https://www.nature.com/articles/s41586-024-08275-2
[2] https://pubads.g.doubleclick.net/gampad/jump?co=1&iu=/6978/reg_offbeat/science&sz=300x50%7C300x100%7C300x250%7C300x251%7C300x252%7C300x600%7C300x601&tile=2&c=2Z3q6sHKFsntpXb-3spzygAAAAMw&t=ct%3Dns%26unitnum%3D2%26raptor%3Dcondor%26pos%3Dtop%26test%3D0
[3] https://www.bbc.co.uk/news/articles/clyx9nv4mleo
[4] https://pubads.g.doubleclick.net/gampad/jump?co=1&iu=/6978/reg_offbeat/science&sz=300x50%7C300x100%7C300x250%7C300x251%7C300x252%7C300x600%7C300x601&tile=4&c=44Z3q6sHKFsntpXb-3spzygAAAAMw&t=ct%3Dns%26unitnum%3D4%26raptor%3Dfalcon%26pos%3Dmid%26test%3D0
[5] https://pubads.g.doubleclick.net/gampad/jump?co=1&iu=/6978/reg_offbeat/science&sz=300x50%7C300x100%7C300x250%7C300x251%7C300x252%7C300x600%7C300x601&tile=3&c=33Z3q6sHKFsntpXb-3spzygAAAAMw&t=ct%3Dns%26unitnum%3D3%26raptor%3Deagle%26pos%3Dmid%26test%3D0
[6] https://www.penguin.co.uk/books/316593/the-world-before-us-by-higham-tom/9780241989050
[7] https://pubads.g.doubleclick.net/gampad/jump?co=1&iu=/6978/reg_offbeat/science&sz=300x50%7C300x100%7C300x250%7C300x251%7C300x252%7C300x600%7C300x601&tile=4&c=44Z3q6sHKFsntpXb-3spzygAAAAMw&t=ct%3Dns%26unitnum%3D4%26raptor%3Dfalcon%26pos%3Dmid%26test%3D0
[8] https://www.theregister.com/2024/10/29/tardigrade_genetics_radiation/
[9] https://www.theregister.com/2024/10/25/epibit_dna_storage_research/
[10] https://www.theregister.com/2024/09/21/human_genome_5d_memory_crystal/
[11] https://www.theregister.com/2024/06/17/researchers_amber_like_polymer_storage/
[12] https://pubads.g.doubleclick.net/gampad/jump?co=1&iu=/6978/reg_offbeat/science&sz=300x50%7C300x100%7C300x250%7C300x251%7C300x252%7C300x600%7C300x601&tile=3&c=33Z3q6sHKFsntpXb-3spzygAAAAMw&t=ct%3Dns%26unitnum%3D3%26raptor%3Deagle%26pos%3Dmid%26test%3D0
[13] https://whitepapers.theregister.com/
Possible reasons for invasions not causing language changes in Britain
The fact that there was a no lasting change of language from the Roman, Viking and Norman invasions in the British Isles IS interesting.
I wonder if this effect could simply have been due to the invaders in these cases being a relatively small part of the population, thanks to the difficulty of assembling a large fleet to cross the Channel combined with communication difficulties due to a lack of common language as well as circumstances such as:
- the Romans being either aristocrats or soldiers living in barracks
- the Vikings being smallish raiding parties
- the Normans being mostly aristocrats and soldiers that couldn't or wouldn't talk to peasants
Re: Possible reasons for invasions not causing language changes in Britain
Are Vikings people who are just really good at using a text editor?
Re: Possible reasons for invasions not causing language changes in Britain
Vikings are the *masters* of a powerful text editor.
FTFY
Re: Possible reasons for invasions not causing language changes in Britain
Vikings did, in fact introduce a good few words into English as a whole and rather more in the old Danelaw. That's because they settled as ordinary members of the population. Romans & Normans were an elite, minimally connected to the population. The Normans contributed a few words on account of their social situation, sheep vs mutton being the best known example. I suppose Latin might have loaned words into Welsh - perhaps any Welsh speaking commentard could give examples.
Re: Possible reasons for invasions not causing language changes in Britain
There's a fair amount of Norse in the English language - more so in northern areas - coming from the Danelaw.
The side-by-side usage of Old Norse and Old English promotes a change from synthetic (use of inflections to denote the relationship of words) to analytical (word order drives meaning) language.
There's a lot of Norman French words in the English language and the Anglo-Norman period sees further moves to analytical.
Old English example:
Fæder ure şu şe eart on heofonum, si şin nama gehalgod. to becume şin rice, gewurşe ğin willa, on eorğan swa swa on heofonum
Middle English example:
Oure fadir şat art in heuenes halwid be şi name; şi reume or kyngdom come to be. Be şi wille don in herşe as it is dounin heuene
The second seems much closer to modern English doesn't it
" The immediate post-war generation of archaeologists, perhaps understandably, disliked the idea of invasions & insisted that nothing could be called an invasion without written evidence which rather restricted invasions to areas and times with a written history"
Citation needed?
Any 1960s archaeology textbook of your choice. More recently Francis Pryor's AD.
Up to a point it was fair enough - invasions had been overworked as an explanation e.g. invasions from Egypt were supposed to explain passage graves until it turned out that passage graves were a lot earlier.
It used to be said that particle physics was like hitting a watch with a hammer and working out how the watch worked by examining the bits. Population genomics seems to me more like collecting a lot of watch bits and working out which of numerous watches each bit came from. As far as I can understand the methods here (which isn't very far as yet) the objective seems to be to reduce the choice of watches.
I'm looking forward to seeing more detailed results. The immediate post-war generation of archaeologists, perhaps understandably, disliked the idea of invasions & insisted that nothing could be called an invasion without written evidence which rather restricted invasions to areas and times with a written history. Roman, Viking & Norman invasions of Britain couldn't be gainsaid but they were against the idea of Anglo-Saxon invasions or folk-movements even though the scanty continental sources, later English and Welsh tradition and the only contemporary insular source, Gildas, all point to such a thing together with the fact that there was a lasting change of language which neither Roman nor Norman invasion managed. Current DNA and chemical analyses are starting to point to genuine folk movements so hopefully this will clear things up.