Some time early in life, we are introduced to the ideas of academic fields interested in the evolution and history of humans. For many, this triggers their first intellectual awakening. In our private conversations, human origins is a subject we’ve returned to a few times. These discussions have been stimulating and often cut to the core of what it means to be human. These ideas have deep implications for how we should think about ourselves as individuals and populations and as a species.
We couldn’t even come close to covering everything in this brief conversation, and there may have been places where we said something unclear, contestable or outright incorrect. So in the show notes here, we’re providing additional information presented in a Q&A format for any listener looking for more related content on human evolution and population histories. This content is based on Manjul’s prep questions and Stetson’s answers. Stetson does his best to answer based on his background in genetics and his reading of various sources. There is some overlap with what actually appears in the podcast as well.
Questions and Answers on Human History:
Human Evolution Narratives
* Can you explain the significance of the “Out of Africa” (OOA) theory and how it has shaped our understanding of human migration?
* Yes, OOA is the standard model for explaining modern human origins. It is still taught in classrooms. The idea is that modern humans emerged from archaic human populations in Africa and then quickly migrated to the Near East and then the rest of the Eurasian landmass sometime between 100-50 kya.
* New data from ancient DNA is complicating this story. The basic issue is that the Near East and NE Africa are a continuous landmass and so genes can flow back and forth. We also know archaic humans had already populated Eurasia prior to the OOA migration and that these populations contribute to our modern human lineage.
* We do know from genomic and archaeological data that human origins begin in Africa, but the extent to which our modern lineage owes itself specifically to African ancestors remains somewhat unclear. The preferred working model today, I believe, is that of deep but weak African structure with likely multiple introgressions from archaic humans.
* From the human origin that is agreed to have started in Africa, how did we get here?
* Think of the broad Human lineage as a trellis that fans out or bunches together at different places.
* If we rollback 1-2 mya, we have an archaic human group in Africa. We don’t know a lot about the genes of these early ancient humans. Some of these groups left Africa and populated Eurasia. This includes groups like Homo erectus and later Neanderthals. At some point we start seeing remains that look like modern humans ~300kya. Things are a little unclear in this period but then between 100-50 kya modern humans sweep up out of Africa/the Near East into the Eurasian continent. From there, we get some mixture with Neanderthals and population bottlenecks (events that dramatically shrink the human populations). Things stay as hunter-gatherer groups moving around a bit until agriculture begins to emerge around ~10kya. Then we get a resettling of Eurasia again by the groups developing agriculture. There are different waves of these groups. One of best studied is a group of pastoralists (a ghost population - meaning a population that no longer exists in unmixed form today) thought to be responsible for the wheel and Indo-European languages called the Yamnaya, who came from the steppe lands north of the Black and Caspian. The Yamnaya swept through Europe and down through some of Asia and have contributed substantially to modern populations in both those regions today. This occurred ~5000 years ago.
* Here is a summary of the population history of Europe.
* Perhaps the best archaeological evidence of early modern humans in Africa is from a partial skull and skeleton discovered in 2017 in Morocco. This finding is 300,000 years old. This is largely consistent with the ancient genetic data, which extrapolates our shared maternal lineage to around 160kya and various regions of the genome can be followed back further to Africa.
* Omo I by Richard Leakey is another example of modern human remains dating back to pre-OOA migrations.
* Unfortunately, the African climate is not hospitable to the preservation of DNA and so much about the emergence of modern humans from archaic humans remains speculation. However, the best available evidence today suggests that modern humans emerged from mixtures of archaic humans in Africa around 300kya or more.
* There were also certainly archaic human groups in Africa 1-2mya that are important contributors to modern humans.
* What are the most significant discoveries in the study of human origins?
* This is of course a judgment call, but Svante Pääbo was awarded the Nobel prize in physiology and medicine in 2022 for developing techniques that allowed for the sequencing of the genome of Neanderthals from a thumb bone recovered from a cave in Siberia.
* Building on this work, the lab of David Reich developed statistical methods that have demonstrated that Neanderthals and modern humans interbred outside of Africa and that lineage populated Eurasia.
* Reich argues the biggest finding is that aDNA has complicated or contradicted most of our traditional narratives about the past. Namely, the idea that populations of the past look like those of the present has been shown to be erroneous. Migration and mixture are also fundamental features of human population-level behavior.
* Another major finding is the existence of “ghost populations” or ancient populations that can be inferred to have existed based on sequencing of ancient genomes but no longer exist in unmixed form today. It is incredible that even a single genome contains a population history due to the “magic” of genetics.
* How do genetics and archaeology complement each other in tracing human origins?
* These fields have been increasingly working in collaboration to refine our narratives about human prehistory and the substructure of contemporary populations. This has upturned a lot of conventional wisdom. Both fields are reliant on each other to push our understanding forward but ancient DNA genetics has proved a powerful tool for confirming past migrations and mixture events between past human groups.
* How do we define what it means to be human from an evolutionary perspective?
* This is a bit of a philosophical question, which runs parallel to the philosophical questions about what defines a species. But generally, the idea is that modern humans are those that both look like us morphologically and have the capacity for language and complex culture. We don’t have a precise definition that everyone accepts. Hence, all the talk about Neanderthals and other ancient humans being a different “species” of humans is often not endorsed by geneticists.
* What are the main challenges in obtaining and interpreting fossil and genomic data related to human origins?
* The first big challenge is actually obtaining the samples. These are rare and precious. There are ~6000 human fossils and ~16000 ancient DNA samples have been sequenced.
* The next is contamination. Microbes set up shop in human remains and when scientists handle the remains they can introduce contamination from their own DNA. There are now intense and elaborate methods used to exclude the microbial contamination and prevent the human contamination. These are significantly methodological innovations.
* Can you share any recent breakthroughs in ancient DNA research that have significantly impacted our understanding of human evolution?
* We are really just beginning to study the evolutionary changes that are responsible for modern human behavior. The evidence we have today suggests that there have been many small changes deep in our history rather than a few large and important changes. To most, this is an unsatisfying answer so I can call attention to the interesting findings concerning a gene called FOXP2.
* Research performed in Paabo’s lab has shown that FOXP2 is largely unchanged along the lineage between mice and chimps until the modern human lineage, where two mutations occurred in that broad human lineage. Moreover, there is a change in FOXP2 that differentiates the FOXP2 gene in us versus Neanderthals. There is some other evidence that suggests that human verbal abilities may have outstripped those of Neanderthals (e.g. methylation signatures on laryngeal soft tissue) despite the comparable brain sizes.
* However, there are some exciting evolutionary stories that have occurred over our species' time. This includes the evolution of lactase persistence after the advent of pastoralism. There was a new genetic change that allowed the post-weening expression of the enzyme that digest lactose in certain human populations that were dependent on milk-producing livestock for vital calories.
* Most human traits are influenced by many genes - what we call polygenic. Polygenic adaptation has been elusive despite some evidence for height, birth weight, head circumference, and hip width.
* On the height finding from recent review:
* “An example comes from research comparing polygenic scores for height between different populations. As described in Coop (2019), several studies (Berg & Coop, 2014; Mathieson et al., 2015; Turchin et al., 2012) identified an enrichment of alleles associated with increased height in Northern European populations and concluded this was evidence of polygenic adaptation for height. To construct polygenic scores, these studies used summary statistics from GIANT, a meta‐analysis of height that combined GWAS data from various European cohorts. However, later studies that used summary statistics from the UK Biobank, a single cohort with a more homogeneous population, failed to replicate the enrichment of height‐increasing alleles in Northern European populations (Berg et al., 2019; Sohail et al., 2019). These later studies found that the SNP associations in GIANT were correlated with loadings on genome‐wide principal components, which indicated the presence of residual confounding.”
* Some hold that the selection on height is still there despite the confounding. The magnitude of the selection is just smaller than originally reported.
Cultural and Social Evolution
* How did early humans develop language, and what impact did it have on their social structures?
* I have to punt on this question. The evolution of language is a huge evolutionary question that has been subject to vicious debate. Based on what we think we know about human evolution, it was probably an incremental and gradual process. It is also unclear how much of language is primed by our genome versus invented as a cultural technology. For instance, do we indeed have a universal grammar to all human language like Chomsky has argued or not?
* There is some evidence to suggest that literate human culture was not evolutionarily anticipated but our brain is flexible enough to adapt to it at the cost of facial reading abilities.
* What can ancient art and artifacts tell us about the cognitive and cultural development of early humans?
* The ancient cultural artifacts we have only date back to roughly 50kya. Before this we don’t have much evidence of cognitive and cultural development despite the genetic data suggesting that it must have been there. This has led a small group to argue that there has been recent and rapid evolution in human cognitive abilities around this time. It has led others to speculate about why this “sapient paradox” may exist.
* Why can Nepali people (Sherpas specifically) operate at high altitude with very low oxygen?
* So in addition to the usual physiological adaption we're all capable of to some extent, certain populations including the Sherpa have specific genetic changes that make them more adapted than others to low oxygen environments.
* Although I was remiss in saying this in the podcast, it is well known that Tibetan altitude adaptation is driven by the introduction of a certain variant of the EPAS1 gene into modern humans by an archaic human group called the Denisovans. This EPAS1 gene variant was then selected for over time after introduction.
* Sherpa altitude adaptation is a great example of how selection can shape a human trait to local environments. Those who were more efficient using oxygen had more children and were more robust than those who couldn't. For Sherpas, it is alleged that a change in a gene called PPARA has contribute to the more efficient at using oxygen and generally more efficient metabolisms. I would guess the EPAS1 variant is present as well.
The Contemporary Relevance of Human Population History
* How can understanding our evolutionary past help address current global challenges?
* Study of the genetic past of humans makes it clear that humans have a tendency to move around a lot. Migration and mixture are fundamental features of being human. There are variably sanguine and cynical takes about this human proclivity that can be gleaned from the genetic data.
* Cultural myths about deep history are often wrong in some way. Much of the variation between groups we see today is fairly recent. This isn’t to say it isn’t ever meaningful to traits. It likely is in certain ways, but our past is simply a lot more complicated than we thought. We need ancient DNA to sort this out.
* Understanding population histories can be important to medical outcomes. Let’s explore one interesting example:
* Members of the Vysya community in Coimbatore, India often cannot efficiently metabolize particular muscle relaxants given as anesthesia during surgery. This is due to a genetic deficiency of the pseudocholinesterase (aka butyrylcholinesterase) enzyme, which is shared by some of Indo-European descent but has been enriched by the endogamous practices encouraged by caste customs. The frequency of the homozygous mutation in the enzyme in the Vysya community is 1 in 24. Subsequently, the Vysya have an approximately 100-fold higher rate of butyrylcholinesterase deficiency than other groups, and Vysya ancestry is a known contraindication for the use of muscle relaxants, such as succinylcholine or mivacurium, that are given before surgery. Source: Reich study
* What are the ethical considerations in studying human origins, especially regarding indigenous populations and their histories?
* Generally contemporary scientists have wanted to respect the indigenous claims over remains; however, it isn’t scientifically tenable in my opinion to simply assume that a group making a claim to indigeneity of a particular region is actually related to the found remains. Subsequently, it seems the ethical thing to do with remains is allow scientists to study them to their fullest but with care and then assess the best course of action from there.
* Alternatively, do the wishes of the dead matter? Does cultural or genetic relatedness have bearing on ancient remains? My default is to indulge curiosity and support scientific knowledge.
* What are the next big questions researchers are hoping to answer about human origins?
* Two things:
* Study the likely many little changes that enabled behavioral modernity. Comparing the Neanderthal and Sapien genomes is a good start here but we'll have to go deeper too. For those interested in reading more, search “human accelerated regions” in Google Scholar.
* Get more ancient DNA from Africa to study the archaic populations so that we can understand the population structure of very early humans in Africa and learn more about what led to the emergence of modern humans. Though it is speculated that it was hybridization(s) between different archaic groups in Africa.
* How might advancements in technology, such as AI and machine learning, revolutionize our understanding of human evolution?
* Advanced statistical approaches have already done a lot for the field as has the rapid decline in the cost of DNA sequencing. However, I think the genAI revolution has the potential to help us learn more about the evolution of intelligence and language. We can study the process synthetically and then compare it to how our brains work.
Recommend Reading
* Who We Are and How We Got Here by David Reich
* Razib Khan’s Unsupervised Learning
* An Owner's Guide to the Human Genome by Jonathan Pritchard
Related Notes from Stetson:
* On Neanderthal Social Isolation
* On Genetic Inequality - Dominant Y Lineages
* On the Divergence of Genealogical and Genetic Ancestors
* On the Debate between Purifying and Balancing Selection
* On Whole-Genome Sequencing of African Populations
* On the Peopling of Europe’s Subcontinent and the Indus Valley
Disclaimer
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