January 2025

Redefining the demise and extinction of the woolly mammoth

The woolly mammoth (Mammuthus primigenius) was a greatly successful species characteristic of the Pleistocene megafauna in Eurasia, roaming around the whole northern part of the continent for millennia [1], reaching up to Mediterranean seashores during their highest expansion range [2], and even migrating to the American continent and again back to Eurasia through the Bering land bridge due to sea level downfall during the last Ice Age [3]. The causes of their final disappearance, first from continental mainland and subsequently from their last northern Arctic refugia remain, however, debated. Dr. Marianne Dehasque shared with us one of her last research studies where she tried to elucidate what happened to the last woolly mammoths at the genomic level [4]. In this way, we can learn unvaluable lessons of how near-extinction events affect animal populations in the present, and improve conservation efforts to preserve endangered species.

Woolly mammoth in the Siberian steppe. Picture created by Beth Zaiken.

 

They first started by selecting 21 woolly mammoths to study, of which 14 were dated between 9.3 and 4.3 thousand years-before-present belonged to a population trapped into the Wrangel Island after it got separated from the Eurasian continent. These individuals lived after the severe bottleneck that happened when the island got isolated around 10 thousand years ago due to rising sea levels. The remaining 7 mammoths found in the Siberian mainland were dated to between 12 to 50 thousand years ago. These two subgroups were considered sufficiently separated in time so as to compare how living in a small isolated island during the last living generations of woolly mammoths would have affected them genetically. In a sense, Wrangel island could have been a heavenly peaceful refuge for the last surviving mammoths, but a genetic hell at the same, with a pervasive accumulating inbreeding effect across generations that might have ultimately caused their final extinction. Was Wrangel island ultimately a sinister trap where woolly mammoths were obliged to extreme inbreeding up until they were rendered biologically unable to reproduce further? Did genomic erosion kill the last surviving woolly mammoths?  

Dehasque and collaborators found proof of an increased homozygosity and genetic deletions in Wrangel island mammoths compared to older mainland relatives, as expected due to loss of genetic diversity after the extreme bottleneck caused by the isolation in a small island up in the Arctic. They argued that this is probably caused by increased inbreeding, i.e. mating between close relatives, where genetic diversity gets eroded and similar genotypes get combined forming long regions of homogenous invariant genomic sequences across the population. This was even more prevalent in regions known to harbor genes crucial for immune response, weakening their ability to adapt to pathogens and derived illnesses.  

However, after the initial strong bottleneck effect, they found weak evidence of sustained genomic erosion, where homozygosity kept accumulating but at a much slower pace. To explain this, they suggest a fast recovery after the initial bottleneck and a subsequent stabilization of the isolated Wrangel island population after around 20 generations, with still some level of inbreeding but mostly due to mating with distant relatives. Interestingly and supporting this hypothesis, they found an increased segregation of mutations with mild deleterious effects, but a reduced proportion of highly damaging polymorphisms in Wrangel island mammoths, a finding that they linked to the presence of purging through strong selection against homozygous deleterious mutations. Paradoxically, this could help the endurance of highly inbreed populations through time.  

Dehasque and collaborators inferred that this population quickly recovered after a strong bottleneck caused by land isolation, initially suffering a steep increase in inbreeding and deleterious genetic load hindering their adaptive abilities as seen in immune-related genomic regions, but progressively recovering to a stable population that survived for millennia thanks to pervasive purging of highly damaging mutations and lowered inbreeding effects. However, as they did not analyze the very last woolly mammoths surviving in the Wrangel island, the final cause of the extinction of the woolly mammoths living in Wrangel island remains, as the authors emphasize, uncertain. It might have been caused by a sudden change in environmental conditions or pathogen outbreak leading to high mortality rates, or maybe the last generations of woolly mammoths suffered again a strong bottleneck effect with increased deleteriousness that rendered them finally unable to recover.

References

1. Nyström, V. et al. Temporal genetic change in the last remaining population of woolly mammoth. Proceedings of the Royal Society B: Biological Sciences 277, 2331–2337 (2010).

2. Álvarez-Lao, D. J., Kahlke, R. D., García, N. & Mol, D. The Padul mammoth finds — On the southernmost record of Mammuthus primigenius in Europe and its southern spread during the Late Pleistocene. Palaeogeogr Palaeoclimatol Palaeoecol 278, 57–70 (2009).

3. Debruyne, R. et al. Out of America: Ancient DNA Evidence for a New World Origin of Late Quaternary Woolly Mammoths. Current Biology 18, 1320–1326 (2008).

4. Dehasque, M. et al. Temporal dynamics of woolly mammoth genome erosion prior to extinction. Cell 187, 3531-3540.e13 (2024).

 

Below, Marianne shared with us further details about her profile, career, prospects and future projects:  

1. Briefly introduce yourself. What is your origin story for how you got into science?
Hi, I’m Marianne, a postdoctoral researcher at Uppsala University in Sweden. My current work focuses on the genomics of feralization in sheep, using both contemporary and ancient DNA. Before this, I completed my PhD at Stockholm University, where I studied the genomics of the last woolly mammoth population on Wrangel Island. If you created a word cloud of my research interests, you’d probably see words like “woolly,” “island,” and “ancient DNA” standing out.

2. How and/or why did you start working on this project?
The mammoth project has already been going on for over 20 years. I joined the team as a PhD student in 2018. I sometimes joke that “I am number four”, referring to being Love Dalén’s fourth PhD student working on mammoths. What makes the Wrangel Island mammoth population so fascinating -aside from being the enigmatic last woolly mammoth population – is how closely their story mirrors the challenges of many present-day species threatened by climate change and habitat loss. This makes the Wrangel mammoths an excellent system to study and test long-standing hypotheses on the evolutionary processes in small, declining populations. The insights we gain can hopefully also contribute to the field of conservation genomics and help us better understand how to protect endangered species today.

3. Were there any major challenges in this project? How did you overcome them?
Like most scientific projects, this one had its fair share of challenges—some bigger than others. One standout moment involves a mammoth nicknamed “Lonely Boy.” I wrote a piece about our adventures with Lonely Boy in The Conversation, but to keep things brief, we invested a lot of time (and money!) into analyzing a precious sample that, in the end, turned out to be a completely average mammoth.

4. What do you think are the main take-home messages of this project?
I would say there are two take-home messages in this project: The first one being that the mammoths on Wrangel Island were not doomed by their small population size. Instead, a sudden and short event likely caused the population’s demise. This challenges earlier hypotheses, suggesting that an accumulation of genomic defect led to the Wrangel mammoth’s extinction. Those earlier studies relied on limited data, such as small markers or a single Wrangel Island genome. In our study, we analyzed a dataset of 21 serially sampled mammoth genomes, providing us a much more complex and nuanced understanding of the mammoth’s extinction. Second, despite quickly recovering from a sudden population decline, the Wrangel mammoths suffered from inbreeding depression for over 6,000 years. This is an important finding for conservation – as it implies that just restoring population size may not be sufficient to ensure a viable population. Instead, active genetic monitoring is essential to safeguard against long-term population bottleneck-related issues.

5. What do you think is missing in the field that you would like to work on?
Most ancient genomic research has focused on SNP’s and small indels, but the world of structural variants remains largely unexplored. I believe that further exploring this type of genetic variation could reveal exciting new insights into evolutionary processes over time.

6. Where do you see yourself in the near future?
In a sunnier place than Sweden. Preferably somewhere with a nice beach.

     

The mysteries of chicken domestication and its worldwide expansion

The domestic chicken (Gallus gallus domesticus) is one of the main sources of animal protein consumed worldwide [1]. Given its importance in the current human diet and food industry, gaining accurate knowledge about the chicken’s origin, domestication process, and global expansion is important for understanding world agrobiodiversity and guiding future breeding and management strategies. However, the birthplace of domestic chickens remained long contested, with studies supporting a Southeast Asian [2] or a South Asian origin [3], while others argued for a Northern China origin [4]. Reanalysis based on modern genomic information led to the identification of the subspecies of red junglefowl Gallus gallus spadiceus as the most likely progenitor of domestic chickens [5], with the domestic lineage diverging around 12,800 to 6,200 years ago.  

In their recent work, dr. Ophélie Lebrasseur and collaborators reevaluated the taxonomic identification, dating, and domestic status of around 600 archaeological chicken remains from 89 countries across Asia, Oceania, Europe, and Africa. By applying a conservative approach that accounted for known biases such as insecure stratigraphic dating, possible species misidentification with the local wild avifauna, and the cultural and environmental context [6], they challenged previous claims that placed the domestication of chickens around the Indus valley or Northern China. Instead, Lebrasseur et al. determined that the earliest domestic chicken remains had been found at the Neolithic site of Ban Non Wat in central Thailand and dated to 1,650 to 1,250 BCE. While this finding does not pinpoint a domestication event at that precise location or time, it implies that domestication occurred later than previously claimed [2,4]. Following their domestication, chickens expanded towards Central China, South Asia, and Mesopotamia by the late second millennium BCE, followed by a western dispersal to the Mediterranean and Africa around 700 BCE [6,7].

Species identification of Argentinian archaeological bird bones using the reference collection hosted at the Fundación de Historia Natural Félix de Azara. Chicken bones were then sent for ancient DNA analyses. With special thanks to Sergio Bogan. Picture by Ophélie Lebrasseur.

 

Moreover, dr. Lebrasseur and collaborators proposed that chicken domestication occurred alongside the dispersal of rain-fed dry rice agriculture in Southeast Asia, whereby land claimed for cereal cultivation and the new environmental conditions it created may have attracted wild red junglefowls. This would have allowed closer interactions between these wild birds and human societies, eventually leading to their domestication through a commensal pathway, and their later dispersal to other regions alongside the expansion of rice or millet agriculture.  

More recently, dr. Lebrasseur has expanded her research interest towards the introduction of domestic chickens to the Americas. In this regard, previous studies questioned the evidence of pre-Columbian domesticated chickens in South American archeological sites, with presumably “chicken” bone remains probably belonging to other endemic wild birds, thus discarding a Polynesian introduction prior to a European introduction of domestic chickens [8,9]. Additional work is currently ongoing using ancient DNA and morphological techniques on chicken-like bones from other archeological sites to confirm their taxonomic identity. These findings will be linked to the societal and cultural context in order to establish a more comprehensive picture of the dispersal of domestic chickens and their roles in local societies across the Americas following their introduction by the Europeans.

References

1. FAO. Agricultural production statistics 2010–2023.

2. West, B. & Zhou, B. X. Did chickens go North? New evidence for domestication. J Archaeol Sci 15, 515–533 (1988).

3. Zeuner, F. E. A History of Domesticated Animals. (Hutchinson & Co., London, 1963).

4. Xiang, H. et al. Early Holocene chicken domestication in northern China. Proc Natl Acad Sci U S A 111, 17564–17569 (2014).

5. Wang, M. S. et al. 863 genomes reveal the origin and domestication of chicken. Cell Res 30, 693–701 (2020).

6. Peters, J. et al. The biocultural origins and dispersal of domestic chickens. Proc Natl Acad Sci U S A 119, e2121978119 (2022).

7. Best, J. et al. Redefining the timing and circumstances of the chicken’s introduction to Europe and north-west Africa. Antiquity 96, 868–882 (2022).

8. Thomson, V. A. et al. Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific. Proc Natl Acad Sci U S A 111, 4826–4831 (2014).

9. Buhring, K. et al. Revisiting the evidence of the Arenal 1 site: Chronologies and human interactions in central southern Chile. The Journal of Island and Coastal Archaeology, 1-24 (2023).

Below, Ophélie shared with us further details about her profile, career, prospects and future projects:

1. Briefly introduce yourself. What is your origin story for how you got into science?
I’m Ophélie Lebrasseur, a zooarchaeologist and palaeogeneticist working primarily on the biocultural history of chickens. My fascination with the past began at the age of seven after visiting a dinosaur exhibition. Granted, palaeotonlogy and archaeology are two different disciplines, and I eventually realised my true passion lay in understanding past human societies. I quickly became enthralled by the world of zooarchaeology, and particularly the study of human-animal relationships. But I wanted to push the boundaries of what faunal assemblages could macroscopically tell us. I hence ventured in the field of ancient biomolecules – specifically ancient DNA. Funnily enough, since chickens are distant descendants of theropod dinosaurs, it seems I didn’t stray too far from my original plan as a seven-year-old!

2. How and/or why did you start working on this project?
The domestic chicken (Gallus gallus domesticus) is the most ubiquitous bird on the planet and a dietary staple in numerous cultures across the world. In Neotropical America, the region contributes over a fifth to global poultry production, despite chickens having only arrived on the continent 500 years ago. This reflects a notable adaptation to new environments and integration within local societies. Yet we know surprisingly little about the circumstances of their introduction, the characterisation of local ecotypes, and the genetic adaptations that have enabled them to thrive across the region’s varied cultural, environmental, and climatic landscapes. Given the crucial role chickens play in the livelihoods of many of the world’s poorer communities, and the growing challenges posed by climate change – and against which the resilience of commercial poultry is questionable –, I became passionate about investigating and understanding the biocultural history and environmental adaptation of local chicken ecotypes on the continent. These populations may hold the key to sustainable poultry production in the future, ensuring food security and safety, and the well-being of communities across the global South.

3. Were there any major challenges in this project? How did you overcome them?
Investigating the introduction of an animal to a new region requires a solid knowledge and understanding of the local fauna. South America presents a particular challenge as it is home to numerous species of tinamous (Tinamidae), some of which are widespread across most of the continent and similar in size to chickens. Yet comprehensive reference collections are often lacking, leading to frequent species misidentifications. We encountered a similar challenge during our re-evaluation of early chicken bones in Asia, where several of the presumed earliest chicken bones were in fact misidentified pheasants (Peters et al., 2022, PNAS). To address and overcome this challenge, I focused on developing my knowledge and expertise of the local avifauna, including identifying species’ diagnostic morphometric and osteological markers, to ensure accurate species identification prior to proceeding with further analyses. Genetic analyses then confirmed my identifications for the most significant and interesting samples.

4. What do you think are the main take-home messages of this project?
Stay tuned for an upcoming publication :)

5. What do you think is missing in the field that you would like to work on?
The bridge between our research, the industry, and policymaking remains critically underdeveloped. This issue is one we are acutely aware of – it was, in fact, the main theme of the 44th conference of the Association for Environmental Archaeology which I attended in December 2024. The way I see it, the challenge lies not so much in how we communicate our findings and more in the nature of the research questions we investigate in regard to how closely they align with stakeholders’ priorities. As researchers, we often pursue questions that inspire us and address significant topics within our fields, highlighting how our results could be used to address global challenges. Perhaps another approach would be to engage and interact directly with the stakeholders (including industry partners) to co-design research questions. By aligning our research interests with industry priorities and, where relevant, national agendas, we could develop projects that are both academically enriching and practically impactful. At least, that would be the ideal outcome. At present, I am strengthening my collaborations with the poultry industry to gain a clearer understanding of their priorities and the insights they would find most valuable. My hope is to develop partnerships that can effectively contribute to ensuring food safety and security through poultry production.

6. Where do you see yourself in the near future?
I am very fortunate to have been offered a permanent research position at the French National Institute for Sustainable Development (IRD) in Toulouse, France, in November 2024. I look forward to developing and leading my own research team where we will work closely with colleagues in South America and Africa. I am also working on enhancing mobility between countries of the global south, and between the global south and the global north, with the aim of advancing capacity building initiatives in zooarchaeology and palaeogenomics in South America and Africa.

7. Free space to tell something you would like to remark.
I am always open to exploring potential collaborations on projects related to ancient and modern chickens (and other birds) in Latin America. I am also committed to supporting capacity building in zooarchaeology and palaeogenomics for researchers from Latin American and African countries. If you have project ideas you would like to pursue but require additional expertise or are interested in organizing workshops to develop specific skills, I would be happy to discuss how we might work together. Please feel free to reach out if this aligns with your interests. My institutional webpage is: https://crbe.cnrs.fr/en/annuaire/lebrasseur/