#denofsecrets

[sickpapes]

Pontus Skoglund, the “den of secrets” interview

For those of you not making deep and beautiful eye contact with Pontus Skoglund right now, let me tell you a bit about the man in question. Pontus is from Sweden. He’s very handsome. His favorite color appears to be...blue. He’s also one of the great young-bucks in the field of modern evolutionary genomics. This field - known as molecular anthropology - attempts to understand how modern humans evolved and migrated into the tapestry that is like, Our Reality. At an accelerating pace, molecular anthropology is yielding huge and trippy insights into the historical shadows that are the pre-recorded modern world. Thanks to improvements in harvesting high-quality ancient DNA, low-cost & extreme-scale DNA sequencing and an ever-expanding collection of ancient remains, this field is going to continue to pop-off insights and Pontus will assuredly be helping forge the way. We sat down with him to discuss his work, deepest insecurities and the state of the field.

Disclaimer: Not only do I love the genetic history of modern humans, but Pontus is clearly the man. I am so very thankful that he agreed to do this interview and share his thoughts with the Sick Papes readership.

[SP]: As we all know too well from the The Mummy trilogy (The Mummy (1999), The Mummy Returns (2001) and The Mummy: Tomb of the Dragon Emperor (2008), if you raid ancient burial grounds for profit there’s a good chance that The Rock or equivalent will return to this world and attempt to fuck you up. What precautions do you and your institution -  Harvard Medical School - take to ensure your safety?

[SP’s note: Pontus was advised by his extensive collection of lawyers not to answer this question]

[SP]: How did you get into the molecular anthropology? Was it through an interest in molecules? Human history? A sheer act of desperation?

PS: I was studying evolutionary genetics, but the fruit fly side wasn't as fun as I thought it would be.  My favorite part was population genetics, and when I realized that population genetics could be used to study Neandertals, mammoths, and sabre-toothed cats I was more than intrigued. Then at Uppsala University in Sweden, there was this guy that had wild hair, a manic laughter, and an office with lots of boxes of human bones and pictures of socialist world leaders covered in glitter. He worked with ancient DNA.

I not very well suited either for the wet lab or the field, but can instead work on questions that people have been asking since the age of exploration using modern data science. In addition to that, there is a multidisciplinary aspect with the humanities (mainly anthropology and archaeology), which is very rewarding.

[SP]: You’ve published an excessive and excessively interesting set of papers. To illustrate your approach and logic, can you take us through your 2015 Nature paper describing evidence for multiple migrations that were responsible for the peopling of the Americas? Why did dudes think there was only 1 migration event to begin with? What evidence do you show for multiple events? Where did you get this data? Were you testing this hypothesis to start with or did you find hints in the data through exploration that led to your insight?

[PS]: This was a rare eureka moment where I was really thinking about other stuff but found a strange pattern and thought "that's strange". Two years of agonizing over the possibility of data artefacts and biases followed, but it turns out to be real.

Basically, if all Native American groups form a single origin (or migration into the Americas) their patterns of genetic variation should be symmetrical with respect to non-Americans. That is not the case, and what doesn't fit is a unique link between indigenous people in the Amazon and  Australia/Oceania. This forces us to think about what is wrong with the established scenario of a single migration through the continental ice sheets of North America. It possibly brings some fringe theories, such as earlier migrations along the west coast, in from the cold.

[SP]: Clearly you are very diplomatic and understanding of your colleagues in the scientific process and unavoidable ensuing errors. But with this work, you must have upset a lot of old people. Do you enjoy upsetting the establishment? How important are established ideas for framing your questions?

[PS:] I feel like my background isn't from the big labs, and I think it is really important that there is a diverse flora of small labs that keep the field vibrant. Hopefully this can form a healthy establishment, that brings out the best of the idea of scientific competition. We are perhaps not there yet in our field, but the case you are referring to was a very positive experience, all groups were just committed to the getting the right information out.

The most I have ever been involved in upsetting the establishment would be during my PhD studies when we were able to show with ancient DNA that farming spread through Europe by migration of people from the Mediterranean, and not as a trade of ideas or local developments. Some in the archaeological community in Northern Europe remain skeptical of this scenario to this day, I heard the other day that the archaeology 101 textbook in Sweden still sticks to the local cultural development model. Luckily, most international archaeologists seem convinced by now.

[SP]: Understanding modern human evolution seems like it requires understanding evolutionary processes across a large range of time scales, from the millions to few thousand years. What techniques to evolutionary geneticists use to analyze these differing time scales?

[PS]: With ancient DNA we can observe evolution directly over the past 50,000 years, and it is really the only way to do that in natural populations. In that sense I think Darwin would have been pretty excited about it. That's the main time frame I work in. For longer time scales we still have to resort to extrapolating from present-day genomes. One of my dreams is to be able to use ancient proteins, which degrade more slowly than DNA, to reach back a few million years, but we are far away from that still.

[SP]: On that note, in the more experimental fields of Biology, there is often a dichotomy between Biologists that develop new experimental tools and those that use working tools to understand systems they know a lot about. How does this work in modern evolutionary genetics? How vital are new statistical and computational tools? Is it good enough to use the old tools on new DNA samples or does the accumulation of new and different data necessitate tool development?

[PS]: What is often most intellectually rewarding is the rare occasions when those two happen at once so a new tool gives a major empirical insight. I have worked quite a lot to develop new population genetic and bioinformatic tools, but am not really a qualified software developer. Right now ancient population genetics has stabilized a bit in the statistical paradigm being used, owing a lot to the work of my advisors David Reich and Nick Patterson, but new and more refined questions will require ways to find answers.

[SP]: That said, would you consider yourself more of a bone master or master boner?

[Interviewer’s note: Pontus, surprisingly, declined to answer this question]

[SP]: I have an aerial question for you. To an outsider, it seems as though there are a handful of historical questions that receive a lot of attention. For example, interactions of hunter gatherers and farmers within Europe or migrations into the Americas or Austronesia. Do you think that there are a fixed, small number of these “great” questions or do think the number of important events and tractable questions will continue to grow as more is gleaned from the archeological record or genetic data itself? What could these as of yet unknown questions be?

[PS]: In some sense that is certainly true, and ancient human DNA will perhaps in part move into the more 'micro' realm of characterising individual archaeological sites. On the other hand there will be a constant push to go further back in time. Ancient DNA has a further perspective in that it is relevant also for studying e.g. speciation, adaptation and extinction, something that is not common right now, but could be where much interesting work will be done in 10-20 years.

I am also really excited about quantitatively integrating different types of DNA: human ancient DNA, animal ancient DNA, isotopic information about diet, and archaeological information, to ask more fundamental questions about the processes that have driven human history.

[SP]: Although a lot of good stuff has happened too, the last 300 years has been quite a colonial cluster fuck. Many indigenous people have been murdered, directly or indirectly. Recognizing the destruction to humanity, what additionally has been lost in terms of understanding the genetics of modern humans?

[PS]: Documenting the history of colonization and other atrocities is one of the useful things population genetics can contribute to. As for the past, I think writing the story of the diverse human groups that ended up not leaving much ancestry in present-day population is perhaps more fascinating, and arguably more important, than focusing on tracing the origins of present-day populations. It is a real opportunity to complete the history books that ancient DNA provides.

In the present-day, population genetic studies of indigenous communities can contribute to inclusiveness in the era of personalized genomics. This is sadly still far off, but I think a real positive effect of participation of these groups in genomic studies is the media spotlight it can provide to historically marginalized groups that have a unique genetic heritage. Examples of this includes the Khoe and San of southern Africa, Native American groups, and many other communities.

[SP]: If you had only 1 long weekend left on Earth, but could have any drug and UNESCO world heritage site for yourself and your crew to party, what would you do? For the record, I’d go amphetamines +  Angkor Wat + dance party.

[PS]: I'll go with SLEEP live at, shall we say Luxor? And Swedish snus.

[SP]: In addition to pre-historic humans, you’ve studied the genetics of dog domestication. Can you briefly describe this process? Is there any historical precedent for “dog vs. cat” people or is this a false dichotomy from day one?

[PS]: Cats probably started hanging around human grain stores in the Near East within the past say ~7,000 years or so, whereas we have some preliminary evidence that dogs might have been domesticated before 20,000 years ago. This is when people started inhabiting really harsh latitudes during the raging ice age. Dogs might have been a killer app of living in these environment, they bark when cave lions come too near, they help hunting, pull your sleds, and have been used a spare food resource. We don't know if this is the truth yet, but ancient genomes will almost definitely tell us soon.