In cold pursuit

Posted on May 28, 2021 by twilightbeasts

From feathered dinosaurs to woolly mammoths, countless animals that no longer live have come to pervade modern popular culture. Snuck into a world of dragons, witches, and ice zombies in Game of Thrones (or A Song of Ice & Fire), the dire wolf recently experienced a slightly confusing reintroduction into the beloved pantheon of extinct megafauna, as it may appear to some to be mythical by association. Dire wolves were very much real, and we have known about them since the mid-nineteenth century. These charismatic canids roamed the Americas and parts of eastern Asia for more than 100,000 years, going extinct early into the Holocene around 9,000 to 10,000 years ago (BP).What were they really like, and why did they go extinct? In answering these questions, we can also begin to explore the diverse ways in which information is gleaned from fossils.

We start our story in the La Brea Tar Pits in Los Angeles, USA, the largest discovered fossil site containing dire wolves, numbering beyond 4,000 individuals. Tar pits form from crude oil seeping up to the earth surface and congealing into asphalt. The La Brea Tar Pits contained the remains of thousands of animals representing several extant and extinct species that fell into and became deposited in the asphalt between 40,000 and 8,000 BP.  Excavations at La Brea began in 1913, and the asphalt-preserved fossils continue to be used to reimagine not just the organisms themselves, but also the world that they inhabited.  

The wall of dire wolf skulls on display at La Brea. This display holds around 400 skulls. (Photo Jan Freedman)

A predator and its prey

One way to get to know an apex predator is through its preferred prey. Many chemical elements exist as multiple, stable isotopes that carry different numbers of protons in their nuclei. For instance, carbon exists as the common type 12C and the much rarer 13C, while nitrogen exists as the common and rare 14N and 15N, respectively. The stable isotope ratios 13C/12C and 15N/14N vary across different kinds of plants based on their environment and how they incorporate the elements from the atmosphere, and in animals depending largely on their diets. Stable isotope compositions of biological tissues such as bone can reconstruct ancient diets and food webs. A 2007 study first identified how isotope ratios in modern wolves are related to that in their prey, beavers and moose. Applying these findings to isotope ratios in the bones of dire wolves and several candidate herbivore prey species from the La Brea Tar Pits, the authors inferred that dire wolves primarily preyed on horses, and to a lesser extent on mastodon, sloth, and grazers such as bison.

A model of a dire wolf on display at La Brea. (Photo Jan Freedman)

We know dire wolves were likely pursuit predators who chased down their prey and attacked with their jaws alone, based on our knowledge of extant wolves and other canids. This has also been verified through fossil evidence. The authors of a 2017 study predicted and found that patterns of skeletal injuries differed between La Brea dire wolves and sabretooth cats, which were likely ambush predators. Sabretooth cats had frequent spinal injuries from grappling with their prey, while dire wolves tended to have high rates of trauma across all four limbs, consistent with chasing down prey.

Clues to extinction

Patterns and frequencies of tooth wear and damage have been found in living animals to be informative of feeding behaviors. A 1993 study brought this understanding to the study of several La Brea carnivores, including dire wolves. The authors found a high frequency of tooth breakage across the carnivores, likely from tooth-bone contact, suggesting greater utilization of carcasses compared to modern carnivores. Was this due to a decline in available herbivore prey in the late Pleistocene, eventually leading to the extinction of these predator species?

To answer this question, a 2002 study compared dire wolves preserved in two La Brea pits dated to ~15,000-14,000 BP and ~13,000-12,000 BP, respectively, and found that carcass utilization actually decreased over this time span. Times appear to have been especially tough around ~15,000-14,000 BP, leading to more complete consumption of prey to avoid scavenging by other competing predators. The subsequent decline in this behavior may reflect dwindling predator densities as dire wolves and other carnivores approached extinction. A 2015 study found a similar temporal pattern, among other findings.

The study investigated several measures of morphological variation using the remains of 83 dire wolves as well as 97 sabertoothed cats from La Brea, spanning the period between 40,000 and 12,000 BP. One of these measures, fluctuating asymmetry, quantifies (to a reasonable extent) developmental instability, the tendency of traits to deviate from the target phenotype. Symmetrical traits such as the left and right sides of the face are controlled by the same genetic and developmental pathways, and any asymmetry implies developmental instability, typically caused by some form of external stress. The study found increasing fluctuating asymmetry in dire wolves over time from 40,000 BP until ~15,000-14,000 BP, possibly in response to environmental stress associated with rapid climatic transitions during that period. This was followed by a decline in fluctuating asymmetry 13,000-12,000 years ago, mirroring the changes in tooth wear and breakage over the same interval. Together, these studies imply that climatic instability leading up to the Holocene put dire wolf populations under stress, likely through disrupting populations of their herbivore prey, which they never completely recovered from. Humans are also thought, quite contentiously, to have played some role in Pleistocene megafaunal extinctions.

A dire wolf skeleton, mounted in pursuit of prey. (Photo Jan Freedman)

A wolf by any other name

We end with a reflection on the evolutionary relationships of the dire wolf. Over the last two decades, enormous advances have been made in techniques to extract preserved DNA from ancient remains. Ancient DNA provides snapshots of the evolutionary past, and in the case of extinct animals, a way to infer their relationships with extant taxa. A 2021 study looked at ancient DNA from dire wolf remains, and found that dire wolves were in fact distantly related to extant gray wolves. The two species had diverged from a common ancestor more than 5 million years ago, and look so similar largely because they convergently adapted to lives of pursuit predation. To place this in context, jackals, coyotes, and gray wolves are more closely related to each other than to dire wolves.

While modern canids like grey wolves and coyotes are known to sometimes interbreed, the study found that this was not the case between dire wolves and grey wolves. Hybridization leads to the introduction of new genetic diversity, which can often help a species adapt to changing conditions. Dire wolves were not beneficiaries of this process as they disappeared along with the prey species they had been adapted to hunting and eating.

Humans have likely been coming across and pondering fossilized remains of extinct animals for thousands of years. Records of such encounters are thought to persist today in the form of mythological beasts reimagined from the fossils, such as giants, griffins, and dragons. Modern day reconstructions from fossil remains are, as we have just seen, much less fanciful, but far more exciting in what they tell us about ecosystems and episodes in evolutionary history that have been lost to time.

Written by Ornob Alam (Twitter @genomeinquirer)

Edited by Jan Freedman (Twitter @JanFreedman)

Ornob is a graduate student in Michael Purugganan’s lab at New York University. His dissertation research examines the demographic and evolutionary history of domesticated Asian rice in the context of past climate change and human migrations.

Further reading:

Binder, W. J., Thompson, E. N., and Valkenburgh, B.V. 2002. “Temporal variation in tooth fracture among

Rancho La Brea dire wolves,” Journal of Vertebrate Paleontology, vol. 22, no. 2, pp. 423–428, Jul. 2002, doi: 10.1671/0272-4634(2002)022[0423:TVITFA]2.0.CO;2. [Abstract only]

Broughton, J. M., and Weitzel, E. M, 2018. “Population reconstructions for humans and megafauna

Suggest mixed causes for North American Pleistocene extinctions,” Nature Communications, vol. 9, no.

1, Art. no. 1, Dec. 2018, doi: 10.1038/s41467-018-07897-1. [Abstract only]

Brown, C., Balisi, M., Shaw, C. A., and Van Valkenburgh, B. 2017. “Skeletal trauma reflects hunting

behaviour in extinct sabre-tooth cats and dire wolves,” Nature Ecology & Evolution, vol. 1, no. 5, Art. no.

5, Apr. 2017, doi: 10.1038/s41559-017-0131. [Abstract only]

Fox-Dobbs,K. F. D.,  Bump, J. K. B. K., Peterson, R. O. P. D., Fox D. L. F., and P. L. K. L. Koch, P. L. K. 2007.

“Carnivore-specific stable isotope variables and variation in the foraging ecology of modern and ancient

wolf populations: case studies from Isle Royale, Minnesota, and La Brea,” Canadian Journal of Zoology,

doi: 10.1139/Z07-018. [Abstract only]

Goswami A., Binder. W. J., Meachen, J., and O’Keefe, F. R. 2015. “The fossil record of phenotypic

Integration and modularity: A deep-time perspective on developmental and evolutionary dynamics,”

Proc Natl Acad Sci U S A, vol. 112, no. 16, pp. 4891–4896, Apr. 2015, doi: 10.1073/pnas.1403667112.

[Full article]

Perri, A. R., et al., 2021. “Dire wolves were the last of an ancient New World canid lineage,” Nature, vol.

591,No. 7848, Art. no. 7848, Mar. 2021, doi: 10.1038/s41586-020-03082-x. [Abstract only]

Stewart, M., Carleton, W. C., and Groucutt, H. S. 2021. “Climate change, not human population growth,

correlates with Late Quaternary megafauna declines in North America,” Nature Communications, vol.

12, no. 1, Art. no. 1, Feb. 2021, doi: 10.1038/s41467-021-21201-8. [Abstract only]

Vanvalkenburgh, B., and Hertel, F. “Tough times at la brea: tooth breakage in large carnivores of the late

pleistocene,” Science, vol. 261, no. 5120, pp. 456–459, Jul. 1993, doi: 10.1126/science.261.5120.456.

[Abstract only]

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A beautiful world

Posted on May 14, 2021 by twilightbeasts

Our planet is remarkable. Think about it for a second. Oceans full of fish, mammals, invertebrates. Land covered by plants, incredible insects, and amazing animals. The skies full of birds, mammals, and insects. All this life around us living, surviving, dying. Millions of different species of all shapes, sizes, and colours sharing this planet with us. Each species unique. Each playing its own role in the complex ecosystems. It is easy for us to take this for granted with the pressures of our daily lives. Stop. Listen to the bird song. Watch the gentle sway of the leaves in the wind. Spend a few minutes looking at that insect: that little creature oblivious to our lives and seemingly frantically carrying on with theirs. We live in a beautiful world.

It has always been a beautiful world. Our blog posts about the animals of the Pleistocene try to share how amazing animals in the not too distant past were. No matter how bizarre. And there were some truly wonderfully weird creatures. Weird to our eyes. For them, they were perfect. Not matter how weird they seem to us, they were well adapted to their environments. They lived. The odd looking chalicotheres, which looked like a mix between a horse and a gorilla. The spectacular deer, Eucladoceros, with remarkable antlers reminiscent of some kind of forest god. And so, so many more. Including this beast, Celebochoerus, the shovel pig.  

Celebochoerus was a genus of pigs that lived in Indonesia. They were around the same size as wild boar today, but the shovel pig had one big difference: the tusks were enormous! Wild boar can be quite ferocious. Dogs that are with the hunting party are often injured, and in the early 15th century people were injured too. Let’s not forget king Robert Baratheon of Westeros was severely mauled on a boar hunt, which was the end for him, and the beginning of the brutal fight for the throne: really, I blame that boar for the whole seven, bloody, seasons. The enormous tusks on Celebochoerus would undoubtably have provided protection against predators. They would have also been useful in moving vegetation and debris when searching for food; giving the name, shovel pig.

The skull of Celebochoerus heekerenis showign those huge tusks. (Image from Museum Geologi, reproduced with permission)

There were two species of this wonderful beast; C. heekereni living on the large Island of Sulawesi in Indonesia, and C. cagayanensis which was discovered fairly recently in 2016, on the larger island of Luzon in the Philippines. Looking at the fossils hints that the shovel pigs ancestors originated in Taiwan, moving into Indonesia, and then into the Philippines. We know it lived from the Late Pliocene around 3 million years ago until the Middle Pleistocene, around 1 million years ago. For a change, it looks like humans were not the reason for this wonderful creature’s extinction. It appears that other species of pigs moving into their environment pushed them to the edge. There are not a huge amount of fossils and mostly from a few sites, so there is still a lot more we can learn about them. I am pretty excited about future fossil discoveries of this beast to give us lots more information.

The robust skeleton of Celebochoerus heekerenis. (Image from Museum Geologi, reproduced with permission)

Other amazing animals lived alongside the shovel pig in Indonesia, including giant land tortoises, dwarf elephants, and crocodiles along with smaller reptiles and mammals. And the shovel pigs were a part of this amazing ecosystem. Surrounded by rainforest and rivers, it was a beautiful unspoilt time. A time that seems so far away. So difficult to imagine animals like our shovel pig trotting amongst the tress. But it was relatively recent. Just a million years. That is nothing on the whole grandiose scale of geological time.

Our planet has always been glorious. Perhaps, some may argue that it was even more beautiful before humans spread across the globe building giant cities, and destroying forests. It probably was. But this is the world we have. We only have one. A single planet. Earth. So many amazing animals have disappeared throughout time. Strange ones, like the shovel pig. Vanished forever. But we are lucky. We have a whole planet full of amazing plants and animals all around us. Take a moment to look. And really see the beauty.  

Written by Jan Freedman (@JanFreedman)

Thank you to the Museum Geologi for allowing us to reproduce their images for this blog.

Further reading:

Groves, C. 2001. Mammals in Sulawesi: Where did they come from and when, and what happened to them when they for there? In Metcalfe, I, et al. Faunal and Floral Migration and evolution in SE Asia-Australasia. CRC Press. Pp. 333-342. [Full article]

Hooijer, D. A. 1954. Pleistocene vertebrates from the Celebes. VIII. Dentition and skeleton of Celebochoerus heekereni Hooijer. Zoologische Verhandelingen. [Full article]

Hooijer, D. A. 1972. Pleistocene vertebrates from the Celebes. XIV. Additions to the Achidiskodon-Celebochoerus fauna. Zoologische Verhandelingen. [Full article]

Ingicco, T., van den Bergh, G., de Vos, J., Castro, A., Amano, N. & Bautista, A. (2016). A new species of Celebochoerus (Suidae, Mammalia) from the Philippines and the paleobiogeography of the genus Celebochoerus Hooijer, 1948. Geobios, 49 (4), 285-291. [Abstract only]

Laurent, A. F., et al. 2018. Synchronous diversification of Sulawesi’s iconic artiodatyls driven by recent geological events. Proceedings of the Royal Society. B. Biological Sciences. 285 (1876). [Full article]

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The World Before Us

Posted on April 23, 2021 by twilightbeasts
The World Before Us by Tom Higham

Tom Higham helps run the Research Laboatory for Archaeology and the History of Art (RLAHA) at the University of Oxford. He has been a pioneer of improving the efficacy and accuracy of radiocarbon dating, introducing methods that are now global standards in radiocarbon work, like the ultrafiltration of collagen molecules and single amino acid dating. His work has been published in every academic and popular venue imaginable, from Science to the super soaraway Sun and everywhere in between. Thanks to dating improvements implemented by Tom and his team, we now have secure chronologies for the extinction of Neanderthals and a host of other Pleistocene megafauna.

I first met Tom as a very green PhD student, way back in 2002. In those heady Oxford days, our ancient DNA group had close ties with RLAHA and we would often hold informal meetings in the legendary Lamb&Flag pub on St. Giles[1]. Tom is a very enthusiastic and effusively friendly Kiwi whose wide-ranging interests were not limited to radiocarbon, but every aspect of life in the late Pleistocene including ancient DNA, stable isotopes and a host of scientific archaeology methodologies. In Science, I’ve found that people who are positively infectious with enthusiasm are the perfect teachers. Simply hanging about with Tom lead to an organic diffusion of knowledge, that taught me an awful lot about radiocarbon, isotopes, Neanderthals and much more. I was delighted when I heard through Facebook that he was using lockdown to write a book, and determined to buy a copy for myself as soon as feasible after publication. Luckily, I was able to source one through another fabled Oxford institution; Blackwells bookshop on Broad street, and Tom was kind enough to sign it for me. “The World Before Us” is a book that crams everything a global expert who has been at the vanguard of many of palaeoanthropology’s biggest breakthroughs of the last two decades can tell us into 300-odd pages of gripping prose.

I’ve devoured it over the last week and this review is an expression of how much I enjoyed reading it. If you have read much sci-comm then you know, as I do, just how much of it is as dry as a ship’s biscuit. The tightrope between giving the reader enough information to be interesting, and imbuing a sense of narrative and flow is a tricky one that I know all too well myself.

Tom’s book describes how he has been involved with globally important research into Neanderthal extinction, the jaw-dropping discovery of the Denisovans, and the unexpected Hobbits of Flores.

In books like this it’s all too easy to produce a dusty tome of sites, dates, and names but that is a million miles away from what Tom has produced. He has injected enough of himself, his wry observations and subtle humour, to make the tangled story of our origins a real page-turner. Discussions of working in the famous Denisova cave are fascinating, and the discovery of “Denny” the F1 hybrid girl between a Neanderthal mother and a Denisovan father is really brought to life. Her whole story was pieced together from a 1” fragment of indeterminate bone sieved from Denisova cave and identified by ZooMS[2].

What’s great about “The World Before Us” is that Tom synthesises many strands of evidence to tell a convincing best-guess scenario about what our relatives and ancestors were up to. A lot of this information has had to be gleaned from fairly dense academic papers and Tom does an excellent job of distilling the vital essences to add to the overall story. Along the way, thanks to his many connections, he calls on various experts who make cameos in the book and give first-person insight into the advances they’ve made.

Overall, the book massively succeeds in its aim of making the latest advances in our understanding of human origins understandable by everyone and does so in a way that never makes it feel hard to comprehend.  Despite being involved in many of the papers that have fuelled this advancement, Tom never makes the prose about himself but is generous with credit to all who have contributed. After finishing the book it feels like you’ve been on a whirlwind ride through all that’s new and exciting in human origins and with a good appreciation of the collaborative nature of science. Tom’s optimism is ever present in the writing and you can palpably sense this when the books ends, all too soon, with the sentiment “if you think this stuff is cool, wait ‘til you see what’s gonna happen in the next ten years!”.

[1] After 450 years of continuous trading in Oxford’s city centre, the Lamb and Flag closed in January 2020, seemingly permanently. How a college as infamously rich and moneyed as St. Johns can allow this shortsighted asset stripping to happen is a mystery to me and many others.

[2] ZooMS (Zoology by Mass Spectrometry) is a technique that uses comparison of bone proteins from small fragments of bone to identify them to species, when comparative morphology is impossible.

Written by Ross Barnett (@DeepFriedDNA)

You can follow Tom Higham on Twitter @TommyHigham

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The forgotten dogs of South America

Posted on March 19, 2021 by twilightbeasts

Abya Yala was the land of dogs for a long time.* This is where they evolved. On a solitary, large landmass drifting through a vast ocean. A landmass that Europeans would later call North America. These very familiar animals evolved around 20 million years ago, where they gave rise to a huge number, and huge variety, of different species.

The family of dogs is much bigger than just our friendly pets (although the variety within our beloved pets is enormous!). They were once a very diverse, very successful, group of carnivores, and are still diverse and successful today. Of the three different families of canids that have lived (the Hesperocyoninae, Borophanginae, and Caninae), only the Caninae survive.

Today, there are 27 different species of canids across the world, including wolves, numerous species of foxes, bush dogs, and of course our pets. They are familiar animals to us (the scientific name for our household dogs is Canis familiaris) and as a family, they have been around for quite some time, evolving around 34 million years ago. They lived solely in Abya Yala, until around 8 million years ago when they moved across the Berinigia land bridge, and into Asia, Europe and Africa.

It wasn’t until around the start of the Pleistocene, around 2.6 million years ago, that canids made their way to South America. This equally large landmass was separated from North America, until around 3 million years ago when under water volcanoes, and huge deposits of marine sediments built up and formed the Isthmus of Panama. A connection linked these two lonely landmasses together for the first time in over 200 million years. They didn’t so much as find each other, rather, the natural movements of our planet brought them together: two lost souls connected at last.

When animals can move easily across land, they will. And they did. They moved across the Isthmus of Panama in their thousands. Animals from South America, like the giant glyptodonts, terror birds, and giant sloths, moved into North America, and animals from the north, like the sabre tooth cats, tapirs, camels and horses moved south. In this mass exchange of wildlife, species of canid also moved down into this new land. And here they flourished. New environments provide new opportunities.

Graphic illustration of what is dubbed, the Great American Biotic Interchange. The formation of the Isthmus of Panama allowed animals to move freely across both continents. (Image Public Domain)

Although canids have been in South America for a relatively short period of time, this is where they are most diverse. There are ten different species living there today. Several are commonly called foxes, only they are not the same species as the familiar red fox we know, only superficially looking like them. There’s also the rather leggy manned wolf (not a wolf, but a completely different genus, but it does have very long legs). And the bush dog, which looks like a cross between a weasel and a miniature bear.

Once canids arrived in South America, they quickly spread and new species evolved. Dozens of species roamed the land during the Pleistocene. One of them was a top carnivore in this new, unexplored land. Discovered in 1891, Theriodictis platensis was one of the largest canids in South America, about the size of a German Shepherd, and it was well adapted to hunting large prey. There were several other large predators in South America along with T. platensis, including several other canid species, the sabre tooth cat (Smilodon populator), jaguars (Panthera onca), pumas (Puma concolor) and the giant short faced bear (Arctotherium angustidens). The Isthmus of Panama brought a whole melange of new predators with it.

The powerful skull of Theriodictis platensis (Image Public Domain)

Fossils of T. platensis have bene recovered from rocks in the Buenos Aires province of Argentina, Bolivia, and southern Brazil. It was relatively widespread, but restricted to the central areas of South America. Associated fossils indicate that this large canid was living on grasslands, hunting camels, horses, deer, and other large herbivores. Their jaws and skulls show that large muscles would have attached, giving this canid a very strong and powerful bite.

This bite may have been powerful enough to crunch through the armour of the mighty glyptodon. Some researchers suggest that these armadillo tanks evolved even more protection after the arrival of these new predators. The range of new carnivores that moved into South American likely pushed this defensive evolution. Isolated bony plates (osteoderms) have been found, which indicate that they were on glyptodonts, but not attached to the main shell. This hints that these isolated osteoderms were to protect the more exposed areas on the body, particularly around the neck. That these new predators caused fairly rapid changes in already well armoured giants, shows that they were quite formidable beasts. This is not all bavardage. At least one glyptodon fossil shows evidence of being attacked by a large predator, which was most likely Theriodictis platensis.

The majority of fossils come from rocks that date to the Middle-Late Pleistocene, around 780,000 – 500,000 years ago. A small number of specimens have been found in older rocks which date to around 1 million years ago. When it comes to extinct species, we can only gauge their span on the planet by the fossil we have found. Fossils of T. platensis show it was around for around just 500,000 years. More fossils in older and younger rocks may show that it was around for longer, but for the minute we know it was on our planet, hunting large herbivores for around half a million years. And then it vanished. We don’t know why. Competition from other predators? Changing environments? Changing climate? One of the great things about palaeontology is that there are still so many questions that will be answered. Sometimes it through new discoveries and fossils. And sometimes the answers are found in collections in museums. It just takes a fresh look at some old bones.

*Postscript: Abya Yala is the name given to the land lived on by indigenous native people. This land was named ‘America’ after Europeans colonised the land. In the late 1490s, it was coined by the German cartographer, Martin Waldseemüller, after the Italian explorer Amerigo Vespucci. Although Abya Yala is used by the Guna people of Panama and Colombia, it is also used by several indigenous groups to describe the continent. In the Guna language it means “land in its full maturity” or “land of vital blood”.

Written by: Jan Freedman (@JanFreedman)

Further reading:

Chimento, N. R., & Donas, 2017. A. First Record of Puma concolor (Mammalia, Felidae) in the Early-Middle Pleistocene of South America Journal of Mammal Evolution. DOI 10.1007/s10914-017-9385-x

Gillette, D.D., Ray, C.E., 1981. Glyptodonts of North America. Smithsonian Contributions to Paleobiology. 40. pp.1–251. [Full article]

Perini, F. A., Russo, C. A. M., & Schrago, C. G. 2010. The evolution of South American endemic canids: a history of rapid diversification and morphological parallelism. Journal of Evolutionary Biology. [Full article]

Prevosti, F. J. & Palmqvist, P., 2001. Análisis ecomorfológico del cánido hipercarnívoro Theriodictis platensis Mercerat (Mammalia Carnívora) basado en un nuevo ejemplar del Pleistoceno de Argentina. Ameghiniana. 38. pp.375–384. [Full article]

Prevosti, F. J., Dondas A., & Isla, F. I. 2004. Revisión del registro de Theriodictis Mercerat, 1891 (Carnivora, Canidae) y descripción de un nuevo ejemplar de Theriodictis platensis Mercerat, 1891 del Pleistoceno de la provincia de Buenos Aires (Argentina). Ameghiniana. 41. pp.245–250. [Full article]

Prevosti, F. J. & Martin, F. M. 2013. Paleoecology of the mammalian predator guild of southern Patagonia during the latest Pleistocene: ecomorphology, stable isotopes, and taphonomy. Quaternary Internatl. 305. pp.74–84. [Abstract only]

Prevosti, F. J., Tonni, E. P., & Bidegain, J. C. (2009). Stratigraphic range of the large canids (Carnivora, Canidae) in South America, and its relevance to quaternary biostratigraphy. Quaternary International. 210. pp.76-81. [Full article]

Soibelzon, L. H. & Prevosti, F. 2007. Los carnívoros (Carnivora, Mammalia) terrestres del Cuaternario de América del Sur. In: Pons GX, Vicens D (eds) Geomorphologia Litoral i Quaternari. Homenatge a D. Joan Cuerda Barceló. Monografies de la Societat d’História Natural de les Balears Special Volume 14, Palma de Mallorca, pp 49–68.

Zurita, A. E., et al. 2010. Accessory protection structures in Glyptodon Owen (Xenarthra, Cingulata, Glyptodontidae). Annales de Paléontologie. 96. pp.1-11. [Full article]

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Nothing but the tooth

Posted on January 21, 2021 by twilightbeasts

Teeth are probably one of the best parts of an animal. They are tough. They Hard. They can chomp down food. What’s more when the animal dies, they stand more of a chance of outlasting the brittle bones. They take longer to weather and break down. They are less of a treat to scavengers, as there is no nice juicy marrow within teeth. And this means that teeth have a greater chance of surviving to become a fossil. And teeth are good fossils. They are very diagnostic. Looking at a tooth shape we can see straight away if it is an omnivore, herbivore, or carnivore, and then with a little work, we can identify the actual species that tooth came from. For a palaeontologist finding a tooth is the jump up with joy moment. The tooth can tell a lot about the animal they have found and with that, the environment it lived in.

In fact, teeth are so diagnostic, that many new species have been named based on teeth alone. A new species of shark that once lived off the coast of Madagascar 40 million years ago was discovered by fossil teeth. One tooth led to the discovery of a new species of mammal relative that lived around 200 million years ago. There are lots more examples. It’s fair to say that palaeontologists get very excited about teeth.

The teeth of the giant extinct armadillo Macroeuphractus outesi have long been known to be very different from other armadillo species. They are sharp and thick, which mean they were strong. Strong enough to eat things other than insects, grasses and seeds. This armadillo was a meat eater.

The skull of Macroeuphractus showing the large sharp teeth. (Image Richard Lydekker Public Domain)

As always, taxonomy with extinct animals can get in a bit of a muddle, especially when there are not abundant fossils to work from. It has been placed in several different groups over time, but recent research shows it to be closely related to glyptodonts and pampatheres rather than other armadillos. Today armadillos eat a variety of foods, mostly insects and grubs, plants and fruit, and sometimes small mammals and lizards. The teeth of our giant carnivorous armadillo suggests it primarily ate meat, and research shows it had a strong, powerful bite. This is unique among all Xenartha (the Superorder which includes sloths and armadillos). Xenartha all sustain themselves on vegetation for the most part, and will supplement their diet with insects, eggs, small reptiles, and in some cases scavenging carcasses. No herbivore is a true vegetarian. 

It’s a very interesting branch on the Xenartha tree of life. Sometime around 9 million years ago, some armadillos found their niche in eating meat. South America was the origins of armadillos, and as a continent separated from other landmasses, life experimented with different adaptations. It is likely that they dug into the burrows of other animals for a nice warm lunch, as their bodies were not built for chasing prey. They were predators, but ambush predators, breaking into the homes of unsuspecting mammals and reptiles, and devouring the occupants.  

Around 3 million years ago, they disappear, just before the dawn of the Pleistocene. Climatic changes and cooling correlate to several South American animal extinctions. As the onset of the Pleistocene began, with its rapidly changing climates, temperatures were starting to cool, which affected vegetation and species which replied on it. Their disappearance is a short time before the joining of South America and North America, which caused numerous extinctions as new animals moved to explore and exploit new lands. With so few fossils found so far, and only in the Buenos Aires Province, I like to hope that new finds will show that this unique beast survived for a little longer.

Written by Jan Freedman

Further reading:

Alberdi, M. T., et al. (1992). ‘Paleoclimatic and paleobiological correlations by mammal faunas from Southern America and SW Europe.’ Proceedings of the 1st R.C.A.N.S. Congress, Lisboa, October, 1992. Pp. 143-149. [Full article]

Cenizo, M., Siobelzon, E., & Saffer, M., .M. (2015). ‘Mammalian predator-prey relationships and reoccupation of burrows in the Pliocene of the Pampean Region (Argentina): new ichnological and taphonomic evidence.’ Historical Biology. [Full article]

Croft, D. A. (2017). ‘Horned armadillos and Rafting Monkeys: The fascinating fossil mammals of South America.’ Indiana University Press. [Book]

Serrano-Fochs, S., et al. (2015). ‘Finite element analysis of the Cingulata jaw: An ecomorpholigical approach to Armadillo’s diets.’ PLOS One. [Full article]  

Vizcaino, S. F., (2009). ‘The teeth of the ‘Toothless’: Novelties and key innovations in the evolution of Xanarthrans (Mammalia, Xenartha).’ Paleobiology. 35(3). pp.343-366. [Abstract only]

Vizcaino, S., F., & de Iuliis, G. (2003). ‘Evidence for advanced carnivory in fossil armadillos (Mammalia: Xenartha: Dasypodidae).’ Paleobiology. 29(1). pp123-138. [Full article]

Posted in Macroeuphractus outesi | Tagged , , , , , | 3 Comments

The most (and least) read posts of 2020!

Posted on January 2, 2021 by twilightbeasts

2020 has undoubtedly been the strangest year for all of us. Trying to carry on with our lives and work has been challenging during a pandemic, and I know that many of us have lost people close to us over this last year. All three of us hope that this year is a much happier and healthier one for all of our readers.

As 2020 ends, we like to share our top 5 blog posts of the last year, and highlight those least read posts as well, to show them a little love. Sit back with a hot chocolate and enjoy the richness of our past.

 Least read blog posts of 2020:

1. A whorl of difference: A tiny Ice Age survivor found itself in a new home, far from home.

2. A test of time: How can some of the smallest organisms in the oceans help us to work out the climate of the past? One of our smallest beasts, with the biggest stories to tell.

3. Time capsules of the Ice Age: How artic ground squirrels can help us to understand environments during the last ice age. Mummified specimens, along with nests open up a window to a world 20,000 years ago!

A mummified Arctic Ground Squirrel from Alaska. 20,000 years ago this squirrel curled up and went to sleep. But never woke up. (Image by Ryan Somma)

4. The ancients of the forests: Some trees in New Zealand are a geed few thousand years old. They are incredibly important to the ecosystems.

5. The fanged beast: Discover the story of the tiny, venomous shrew.

The most read blog posts of 2020:

1. The stuff of night-mares: One of the largest species of horse to have existed. This post is no one trick pony.

2. Just like the weather: A guest post by Ted Rechlin provides an amazing view of North America with his unique illustrations.

3. America’s Ass: I was quite pleased with the title of this post! And it made it into the top 5! Read to find out what it’s about!

America’s ass, Hippidion, with it’s short, stocky legs, and prehensile upper lip. (Image Twilight Beasts)

4. A very brief introduction to mammoths: It’s all about the mammoths. All 10 species of them!

5. The evolutionary history of extinct and living lions: Latest genetic research by our very own Ross and pals has helped to understand the relationships between living and extinct lions.

From the three of us at Twilight Beasts, we wish you a very healthy and happy 2021. Thank you for continuing to support the work we do on our blog highlighting the amazing diversity of our recent past. We look forward to sharing lots more beasts with you!

Rena (@JustRena), Ross (@DeepFriedDNA) and Jan (@JanFreedman). Follow us on Twitter  (@Twilightbeasts)  and Instagram (@TwilightBeasts)

Posted in Arctic Ground Squirrel, DNA, foraminifera, Kauri tree, Sabre tooth Cat, Shrew, Woolly Mammoth | Tagged , , , , , , , , , , , , , , , , , , , | 1 Comment

Marching up the wrong tree

Posted on December 21, 2020 by twilightbeasts

Before Darwin published his theory of evolution through natural selection, On the Origin of Species, evolution wasn’t a new concept. It had been discussed by many different people of science as early as the Ancient Greeks. It was how evolution happened that no one was able to explain satisfactory until Darwin (and Alfred Russel Wallace, who independently came to the similar theory). When it was published, it caused a huge stir. The Victorians couldn’t break away from their long-held beliefs that God had created ‘man’ in his image, and that humans were separate from the animal kingdom. Presenting this valid theory of evolution would sever the power of the Church, which at the time was the head of most things and most people.  In anticipation for backlash against Darwin, his close friend, Thomas Henry Huxley, wrote to him ‘I am sharpening up my claws and beak in readiness.’ 

I’m a little fan of Thomas Henry Huxley. Despite being well-known for his quick wit and sometimes fearsome demeanour, he was a loving family man, and a very good friend to those he liked. He wrote numerous natural history books, with the aim of making science accessible to the non-expert. One of these, Man’s Place in Nature (1863), focuses on human evolution and our common ancestor. In it, there is a famous illustration by Benjamin Waterhouse Hawkins, which shows the skeletons of a gibbon, orang-u-tan, chimpanzee, gorilla and human.

Tby Waterhouse Hawkins
Benjamin Waterhouse Hawkins illustration in Huxley’s Man’s Place in Nature. (Image Public Domain)

I’ve noticed that this illustration does looks rather similar to The March of Progress, an image that has fed to the misunderstanding of human evolution, and has been written about numerous times by many great science writers (including Stephen Jay Gould and Riley Black). Originally called The road to Homo sapiens, this iconic image was commissioned for Early Man, one of a series of books by Life-Time Books. It shows 15 extinct primates lined up from left to right as if one species evolves into the next. A ladder of human evolution, with the magnificent Homo sapiens at the very pinnacle. It is of course wrong. But that hasn’t stopped it being reused and rejigged for a myriad of different uses from advertising to prints on T-shirt. It is so popular and constantly used in mainstream media because it is so simple: one species evolves into another, better species: humans are at the end of this ‘progress’.

The March of Progress
The March of Progress, by Rudolph Zallinger. (Image Public Domain)

Some years ago, historian Jennifer Tucker suggests that the image from Man’s Place in Nature actually does indicate evolution, and highlights, the ‘chain of being’, which is a Christian thought of a hierarchical structure in nature, with minerals and plants under animals, and animals under humans, and humans being at the top, just below angels and God. The ‘chain of being’ was first thought of by Ancient Greek philosophers, and adapted in the Middle Ages to focus on God’s main creation: humans. Whilst there are similarities between Huxley’s skeletons and March of Progress, I can’t see it illustrating humans at the pinnacle of evolution: Huxley wasn’t one to jump onboard the Christian bandwagon, and he understood Darwin’s ideas well, having read proofs of his book and discussed them with him in letters and in person. The illustration was a comparison of the skeletons of apes, not an evolutionary diagram, and Huxley makes no reference to it being such in Man’s Place in Nature.

I wanted to find out if the March of Progress was inspired by this the Waterhouse Hawkins illustration. The art work was created by Rudolph Zallinger, who painted the beautiful Age of Reptiles mural at the Yale Peabody Museum. I contacted the museum at Yale to see if they knew any more about the March of Progress illustration, and I was introduced to Zallinger’s daughter, Lisa. Sadly we don’t know what inspired him: “…it is tough to say what my father actually drew from or referred to in order to depict that March. We do not know.”

But, Lisa gave a lot more information about the background into the development of this art. The illustrations were based on the science known at the time, as Lisa told me in an email: “…he consulted many of the prominent anthropologists and scientists at Yale for assistance. He was very keen on representing all we knew about the various [hominins]…both in terms of dating, which came before the other in the sequence, and in terms of the bones of each that had actually been recovered.”

Zallinger’s original ideas for illustrating for this Time-Life Book were very different to how they ended up: “His initial drawings were actually groupings of these bones, next to a representation of what that particular [hominin] might have looked like.” He worked with scientific colleagues to illustrate correctly the pose and posture of each one. The Editor for the Early Man book wasn’t keen on Zallinger’s ideas: “the editor did not believe that these depictions would be compelling or striking enough to excite the readers. It was the editors suggesting that they be depicted in a ‘March’.” But Zallinger wasn’t just an artist, he knew about evolution, and his illustrations were always based on the most up to date scientific knowledge of the time. “My father was not really keen on this portrayal, because he was already very aware that [hominin] evolution was more likely akin to the branching of a tree rather than a straight, linear march, so he resisted this depiction. The editor won out, however, and the iconic image was born.”

Discovering the background into how this renowned illustration was conceived is as fascinating as the art itself. Despite Zallinger working closely with artists, and having a good understanding of evolution, it was the need for something to excite readers, and something that would be visually easy to understand that won the day. This one decision has created perhaps the biggest, most dangerous, misunderstanding of evolution that has ever existed. In all its simplicity, it shows progress. An improvement from what came before. The idea that animals get better as they evolve is wrong. Every animal and plant alive today is just as evolved as each other. None is more ‘primitive’. None is ‘simple’. And certainly none are inferior to others. Each is specially adapted for their environment, some more specialist than others, and some more generalist.

Evolution is quite simple when you break it down. When an egg is fertilised, genes from the mother and father are passed on. Sometimes, small changes can happen where DNA doesn’t replicate exactly as it should have, and these may create new genes for new features (a slightly longer beak for example). If it is harmful, then the young animal won’t survive, and that trait is lost in the population. If it proves useful (a slightly longer beak could mean it can get food from a new place), this trait is passed down to the next generation, where eventually the whole population has it, and a new species is born. We can look at fossils, and even genetics, to see the evolution of species in the past. Humans are no different. Our species evolved around 300,000 years ago in Africa, and our family was once more diverse than you can imagine.

The many different species of humans going back 1 million years. Notice how there were several different species on our planet at once. (Image from Galway-Witham, Cole and Stringer, 2019)

There were dozens of different species of hominins (upright walking apes), many of which lived alongside others. It wasn’t a ladder with one species evolving straight into the next, it was a tree; a big, bushy tree. As small populations moved out and explored away from other populations, they adapted to the different environments. Small changes, passed down through their genes, allowed them to survive better in these new environments where they became a new species. It may be a little more complicated because some species were still mating and mixing genes, so anthropologist John Hawks says it was more like a big river delta.

We were never inevitable. Steven Jay Gould once wrote that if we were to go back to the beginning of life and start it all over, life today would be very different, and there would be no humans around. That’s a big thing to think about. We are not special. We are not better, or ‘higher’ than other animals. Evolution was not primed to make us here today. We are just here. Now. But, there is something special about us. We have the power to change our environment around us. Not just locally, but globally. Presently we are taking advantage of that environment, destroying it, and causing the extinction of countless species every year. Species that have evolved and adapted over millions of years. But, we can use that power, our understanding of our actions, to protect this beautiful, fragile planet we live on. There is no march of progress. There is no ‘road to Homo sapiens’. There is Earth, and the immeasurable different types of beautiful animals and plants that we share the planet with. 

Written by Jan Freedman (@JanFreedman)

Further reading:

Posted in Homo sapiens | Tagged , , , , , | 3 Comments

G(e)nomic Wisdom

Posted on December 4, 2020 by twilightbeasts

When I first started doing ancient DNA way back in two thousand and [polite cough], every base pair was a win. Nature papers were published with less sequence than you’d now expect a fresher to produce in their first lab practical. The exciting thing about being in a new and expanding field was the way in which new records were constantly being broken, week by week. The first ancient mitochondrial genome. The first middle Pleistocene DNA, the first nuclear DNA, the first time-stamped dataset, the first Neanderthal genome. All of these ground breaking studies were published while I was a young PhD and post-doc. All of them received enormous amounts of publicity, and rightly so. Each pushed the boundaries in a way that only new research techniques can. My very first paper was published in a reasonably high profile journal and consisted of only a couple of kilobases of data. You’d be lucky to get that published in a Christmas round robin these days.

I distinctly remember lab meetings as a young PhD where serious discussions happened about whether we would ever be able to produce an ancient nuclear genome. And this was amongst other ancient DNA specialists. We just didn’t know. My own early work painstakingly teasing a few base pairs of ancient mitochondrial DNA out of well-preserved sabretooth fossils, while momentous at the time, definitely got my mind spinning over whether one day we would ever get a complete nuclear genome from any extinct cat. While the mitochondrial DNA can tell us about maternal lineages and some demography, the nuclear DNA is the real deal. This is the DNA that is inherited from both mother and father and codes for practically everything that makes up an organism. Whether hair is long or short, patterned or plain, dark or light. How each part of the organism integrates with the whole. The nuclear DNA is the blueprint for life itself and can tell us about phenotype but also about population change, population size, and evolutionary selection pressures, amongst many other things.

Periodically, as sequencing technologies have progressed, I’ve revisited the idea of getting complete genomes from ancient cats. Earlier this year we published the first ancient genomes from a range of extinct lions [de Manuel, Barnett et al.]. But throughout all this, one species has exerted a siren call over me. My favourite extinct species, a ghost of the ice age steppe, and shoe-in for most impressive cat ever to have lived. I’m talking of course about our old friend the Scimitar cat, Homotherium latidens.

We have recently [Westbury, Barnett et al. 2020] published the first ancient nuclear genome of a sabretooth cat. The work is intimately tied to the work I did on ancient lion genomes while working as a postdoc in Copenhagen on a Marie Curie research fellowship. The MCRF work had me focusing on lion genomics, including that of the cave lion (Panthera spelaea). To get good samples, I relied on my friend Dr Grant Zazula who is the state palaeontologist for the Yukon government. He was able to send me some fresh cave lion bones straight out of the Yukon permafrost. These ancient bones had been on ice for 20 thousand years and had excellent DNA preservation. Getting genomes from ancient bones involved first grinding up small bits of them and applying various bucket chemistry tricks to remove the protein/fat/mineral content to leave the DNA behind. This DNA then gets chemically joined to artificially produced DNA that incorporates various binding sites and a unique DNA barcode that allows each fragment to be reliably separated out. This soup of barcoded DNA bits is known as a library, and can be amplified by standard PCR methods and then run on a pyrosequencing machine to produce billions of reads of DNA that represent all the DNA in your extract. Once the initial library is created it will be sequenced as a matter of course to check what percentage of the extracted DNA is actually from the organism you are interested in versus background DNA from contaminants/humans/bacteria/fungi. Obviously the higher percentage of organismal DNA you have to start with the easier (and more importantly, cheaper) it will be to generate enough sequence data to stitch together a complete genome. For some of the cave lion bones Grant sent me, we got phenomenal levels of endogenous content, and those samples ended up on the lion genome paper. One of the samples was a little different though. When I got back that first initial library sequencing, I was sitting on my sofa at home, using my laptop to check how much lion there was in the mix. This involved comparing all the tiny, barcoded fragments to a reference standard of a modern lion mitochondrial genome (although we were ultimately interested in the nuclear genome, comparing how much mtDNA is in the library is easier to do and gives an idea of overall endogenous content that is reliable enough). While sitting and looking at all the snaking lengths of A, G, C, and T in their multi-coloured formatting I noticed something that made me sit bolt upright and nearly knock my laptop off my knees. One tiny corner of the mtgenome of the lion is seared into my mind nearly as deeply as the opening lines of Genesis. The sequence of lion ATP8 was part of the very first lion DNA I ever sequenced for my PhD and I long ago lost count of how many hours I have spent reading, and rereading, the unique sequence of this gene to check and double check that my results were good. It’s as known to me as my first address, my mother’s maiden name, my first pet. I’m never going to forget it. What shocked me into nearly dropping my laptop off my lap is that I recognised that the library sequence I had generated was not cave lion ATP8 but belonged to another cat that over the years I had known almost as intimately. The absence of just three basepairs at a critical point in the ATP8 sequence made all the hairs on the back of my neck stand to attention for I knew that only one other species had that particular deletion: Homotherium.

This bone was not a cave lion. It was a scimitar cat. One of only a handful ever recovered from the Yukon region. And what’s more it was phenomenally preserved. I think I made the decision there and then that we had to try and sequence this sample more fully and get the total nuclear genome out. Over the next six years, that’s exactly what we did, thanks to the generosity and enthusiasm of the Copenhagen Centre for GeoGenetics leader Tom Gilbert and many working members of the group. To name just two, Dr. Marce Sandoval-Velasco was crucial in generating more libraries of Homotherium after my fellowship had ended. Dr. Mick Westbury had the skills and enthusiasm to take the raw genomic data Marce and I generated, and piece it back together into a coherent whole. He also had the talent to apply the latest genomic analyses to the dataset and finally resolve some of the mysteries that shrouded Homotherium.

We were able to use the nuclear genome in a number of interesting ways. First of all, we were able to give an accurate date for when Homotherium, and by extension all the sabretooh Machairodontinae subfamily separated from the modern cats. Palaeontology had placed Homotherium, Smilodon, Xenosmilus and a bunch of other genera on their own twig of the cat family tree. We had previously estimated the separation using the mitochondrial genome but this can give false inferences if there has been any hybridisation (as seen extensively in modern cats, and our own human lineage) or sex-biased dispersal (e.g. if females stay in one place and males travel long distances between groups, as seen in lions). The nuclear data gave a fairly tight estimate of 22.5 million years (also within the bounds estimated from the mitochondrial genome previously) which puts the split pretty squarely at the Oligocene/Miocene boundary or beginning of the Miocene. Immediately, this suggests that the split between machairodonts and felines could be part of larger ecological processes happening at this geological turning point.

A phylogenetic tree based on nuclear data showing the position of Homotherium between the felinae and the Hyaenidae.

Tied into this, we were very interested in testing whether we could detect any signs of hybridisation between Homotherium and other felids that it would have encountered when alive. Pleistocene Homotherium ranges would have overlapped with cave lions (Panthera spelaea spelaea), American lions (Panthera spelaea atrox) leopards (Panthera pardus), tigers (Panthera tigris), and jaguars (Panthera onca), showing how global its distribution was. We see signs in the nuclear genome of modern cats that there has been admixture between lions and snow leopards, lions and tigers, lions and jaguars, and various combinations of their ancestral lineages. So, clearly big wild felids are not super discerning in who they mate with and if we could find signals of admixture between sabretooths and Panthera cats that could tell us something pretty interesting.  However, in complete contrast to the Panthera cats we found no signal of any hybridisation in the Homotherium genome. It seems the scimitar cat either kept completely to itself, or any signs have been completely purged from the genome after the fact. Sad to think we never had any baby sabre-toothed lions.

Using some fancy statistical inference methods we were also able to look at demographics (population change) in Homotherium. The basic theory is that population size and genetic diversity are intimately linked (this makes intuitive sense, the larger the population the more mutations are likely to creep in). Reconstructing this from the nuclear genome of a single individual sounds strange, but remember that each genome contains information on the diversity of the mother and father as we inherit one copy of each gene from both. The appearance of heterozygosity (where DNA differences between the gene from mother and father are found) tells us about genetic diversity and hence population size. Intriguingly, despite being just about the rarest species in the Pleistocene fossil record, Homotherium seems to have had an effective population size comparable to lion, leopard, jaguar and tiger, and much greater than the cheetah or Iberian lynx. Something doesn’t add up. Maybe it’s just that because fossil cats are difficult to tell apart from most of their bones that there has been gross misidentification and all those missing Homotherium have been shut away in drawers full of cave lion or Smilodon.

Graphic representation of nuclear autosomal heterozygosity (proxy for population size) compared between Homotherium and some species of living cat.

Another potential explanation is taphonomy. Maybe Homotherium just mostly lived in places where fossilisation was exceptional and the few scraps we have are from very lost individuals.

However, the most likely explanation is that Homotherium simply lived a very mobile life over its enormous range and this inflated the genetic diversity present in its genome.

To me, the most fascinating aspect of our genomic work has been our attempt at getting information on the phenotype from our long dead gene reads. At the moment this feels very primitive, but like all first steps it has the potential to go somewhere wonderful. We looked at which regions in the Homotherium genome were under positive selection (basically, which parts of the genome have changed and produced functional differences when compared to the same part of the genome in closely related species). When we did this we saw that genes involved with some pretty interesting things seem to have been pushed hard during the scimitar cats evolution. There were genes involved with vision and circadian rhythm, strongly suggesting that Homotherium was a diurnal hunter i.e. one that was active during the daytime and needed exceptional eyesight. There were genes involved with fat-burning, oxygen processing, respiration, and the vascular system pointing towards an active lifestyle of fast pursuit of prey similar to the cheetah or wolf, rather than the ambush hunting style of most cats. There were tantalising hints of something interesting going on in genes associated with increased sociality in model organisms, maybe pointing to Homotherium as a pack animal that could live in small hunting groups.

A graphical representation of which Homotherium genes we found under positive selection and what aspects of biology they are associated with in model organisms. 

Unfortunately we weren’t able to recover to a decent standard some of the genes we know are involved with coat colour and appearance in cats. Genes like MC1R, ASIP, SLC45A2, TYR, FGF5 could have given us amazing insights into the life appearance of sabrecats, which would do so much to place them into their extinct niche. Modern big cats are almost entirely defined by their pelage (their skeletons are practically identical, with only minor differences) and the difference between lion and tiger is nearly all in the mane or stripes.

So, there it is. 22 year old me is faintly impressed by 40 year old me, in having a large part to do with the first sabretooth genome. May all of you stick around long enough to see some of your own dreams come to life.

A wonderful reconstruction by Velizar Simeonovski of a pair of Homotherium latidens hunting a caballine horse during the boreal winter daytime. Painting was commissioned by us to showcase some of the inferences of our paper.

Written by Ross Barnett (@DeepFriedDNA)

Further Reading:

Anton, M., M. J. Salesa, A. Turner, A. Galobart, and J. F. Pastor. 2009. “Soft tissue reconstruction of Homotherium latidens (Mammalia, Carnivora, Felidae). Implications for the possibility of representations in Palaeolothic art.” Geobios no. 42 (5):541-551. [Abstract]

Barnett, R. 2014. “An inventory of British remains of Homotherium (Mammalia, Carnivora, Felidae), with special reference to the material from Kent’s cavern.” Geobios no. 47 (1-2):19-29. [Full Text]

Barnett, R. 2019. The Missing Lynx. London: Bloomsbury.[Book]

Barnett, R., I. Barnes, M. J. Phillips, L. D. Martin, C. R. Harington, J. A. Leonard, and A. Cooper. 2005. “Evolution of the extinct sabretooths and American cheetahlike cat.” Current Biology no. 15 (15):R589-R590.[Full Text]

Barnett, Ross, Michael V. Westbury, Marcela Sandoval-Velasco, Filipe Garrett Vieira, Sungwon Jeon, Grant Zazula, Michael D. Martin, Simon Y. W. Ho, Niklas Mather, Shyam Gopalakrishnan, Jazmín Ramos-Madrigal, Marc de Manuel, M. Lisandra Zepeda-Mendoza, Agostinho Antunes, Aldo Carmona Baez, Binia De Cahsan, Greger Larson, Stephen J. O’Brien, Eduardo Eizirik, Warren E. Johnson, Klaus-Peter Koepfli, Andreas Wilting, Jörns Fickel, Love Dalén, Eline D. Lorenzen, Tomas Marques-Bonet, Anders J. Hansen, Guojie Zhang, Jong Bhak, Nobuyuki Yamaguchi, and M. Thomas P. Gilbert. 2020. “Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.” Current Biology. [Full Text]

de Manuel, M., R. Barnett, M. Sandoval-Velasco, N. Yamaguchi, F. G. Vieira, M. L. Zepeda Mendoza, S. Liu, M. D. Martin, M. H. S. Sinding, S. S. T. Mak, C. Carøe, S. Liu, C. Guo, J. Zheng, G. Zazula, G. Baryshnikov, E. Eizirik, K. P. Koepfli, W. E. Johnson, A. Antunes, T. Sicheritz-Ponten, S. Gopalakrishnan, G. Larson, H. Yang, S. J. O’Brien, A. J. Hansen, G. Zhang, T. Marques-Bonet, and M. T. P. Gilbert. 2020. “The evolutionary history of extinct and living lions.” Proceedings of the National Academy of Sciences of the United States of America no. 117 (20):10927-10934.[Full Text]

Meachen, Julie A. 2017. “Ancient DNA: Saber-Toothed Cats Are the Same Beasts After All.” Current Biology no. 27 (21):R1165-R1167. doi: 10.1016/j.cub.2017.09.024.[Full Text]

Paijmans, J. L. A., R. Barnett, M. T. P. Gilbert, M. L. Zepeda Mendoza, J. W. F. Reumer, J. de Vos, G. Zazula, D. Nagel, G. Baryshnikov, J. A. Leonard, N. Rohland, M. Westbury, A. Barlow, and M. Hofreiter. 2017. “Evolutionary history of sabre-toothed cats based on ancient mitogenomics.” Current Biology no. 27 (21):3330-3336.[Full Text]

Widga, C., T. L. Fulton, L. D. Martin, and B. Shapiro. 2012. “Homotherium serum and Cervalces from the Great Lakes Region, USA: Geochronology. morphology and ancient DNA.” Boreas no. 41 (4):546-556.[Abstract]

Posted in American Lion, Cave Lion, Cheetah, DNA, European Jaguar, Leopard, Lynx, Sabre tooth Cat | Tagged , , , , , , , , | 10 Comments

The Story of the King Rabbit

Posted on September 2, 2020 by twilightbeasts

‘And he said, “Very well, I will bless your bottom as it sticks out of the hole. Bottom, be strength and warning and speed for ever and save the life of your master. Be it so!” And as he spoke, El-ahrairah’s tail grew shining white and flashed like a star: and his back legs grew long and powerful and he thumped the hillside until the very beetles fell off the grass-stems. He came out and tore across the hill faster than any creature in the world.’

Dandelion telling the story of ‘The Blessing of El-ahrairah’

In Watership Down, 1972

And so, this is how rabbits told the story of how they came to be. Frith created rabbits for speed and cunning to escape from the ‘Thousand Enemies’. Many people have looked at the religious links in Watership Down, but recently the daughters of the author, Richard Adams, revealed the truth: “It’s just a story about rabbits.” And it is: a story about rabbits. Rabbits who have created a history of how they came to be on Earth. (It is a wonderful tale, and I will admit the animated film brought an awful lot of tears.)

Dandelion told many stories to Hazel, Fiver, Bigwig (oh, big, soft-hearted Bigwig) and the other rabbits of the warren. The story of Rowsby Woof and the Fairy Wogdog, The trial of El-ahrairah, and more helped the rabbits link the real world to their lives. If they had known about this beast, I imagine Dandelion would have told the The story of the King Rabbit.

The reality would have been even greater than Dandelion’s legend.

The Watership Down movie poster, with poor Bigwig in a snare. (Image Public Domain)

The story would, as a good tale does, start on an island. Islands are wonderful places for species to evolve into some extraordinarily strange shapes and sizes. With more food around and less predators, small animals tend to evolve to be bigger, and larger animals evolve to be smaller. We’ve seen this numerous times, with dwarf elephants and dwarf hippos on Crete, the giant dormouse, the dodo, the enigmatic mouse-goat, and even within our own Genus, with the ‘hobbit’ Homo florensiensis. It’s actually a real rule known as Foster’s rule: given enough time, and separated from mainland populations, large animals will shrink over time, and small animals will get bigger over time.

Around 6 million years ago the Mediterranean Sea was empty. Temperatures were hot, and there was no Strait of Gibraltar, which meant as the sea evaporated, it wasn’t replenished, so slowly it dried out. This large exposed land was connected to Europe Syria and North Africa, and thousands of animals lived here. Periodically, it was flooded, until the small Strait of Gibraltar, just 9 miles wide, opened up and let waters from the Atlantic Ocean flow in and keep the Mediterranean Sea, well, a sea.

Several islands formed as the Mediterranean was flooded. Here, many animals were separated from populations on the mainland, and separated they were free to evolve to their new environment. And here one rabbit would become a king.

Map of the Mediterranean Sea. (Image Public Domain)

Over a hundred years ago, Dorothea Bate explored Mediterranean islands in the search for fossils. She discovered many extant and extinct animals, and opened up a new world of island fauna never seen before. Since then researchers are still visiting the cave sites Bate explored and excavated. And they are discovering new things. At a site on the small island of Minorca, Spain, in the 1980s researchers excavated a new fissure at one of Bate’s original cave sites, and found remains of an unknown rabbit. It would be more than 30 years before it would be properly described for science. 30 years before the king rabbit would be unleashed onto the world.

When the fossils were examined it was clear that it was a new species of rabbit, Nuralagus rex (‘the Minorcan king of the hares’) . It was ten times larger than the European rabbit. Ten times larger. That’s a pretty big rabbit. The bones gave even more surprises. Looking at the skull in detail, it appears that Nuralagus had much smaller ears than rabbits you are familiar with today. The vertebrae showed that it’s back was much stiffer than other rabbits, suggesting strongly that this giant was a very poor runner, if it ran at all, and couldn’t hop. What’s more, the feet bones indicated that it wasn’t adapted to digging burrows. This giant rabbit (and it was a rabbit) couldn’t be more un-rabbit like.

Our strange giant rabbit, Nuralagus rex, as big as a sheep.

Around 5 and a half million years ago, one population of rabbits became trapped as the Mediterranean Sea flooded. (Based on the morphology of the fossils, and the time periods the fossils have been found in, the more probable rabbit was Trischizolagus.) There was more food around, so this rabbit got bigger. With no predators, speed and large ears were lost throughout generations. We don’t know exactly when this rabbit vanished, and we need more fossils to help us understand when and why it became extinct. What we do know is that it was a rabbit never seen before, or since.

The Story of the King Rabbit is almost like something that Dandelion would tell to the group at Watership Down, and no doubt made Bigwig see a little of himself in the king. But it was real. And it lives on through the legacy of Dorethea Bate who opened up cave sites that are changing everything we thought we knew about the Mediterranean’s extinct creatures.

Written by Jan Freedman (@JanFreedman)

Further Reading:

Bover, P., et al. 2014. ‘The Late Miocene/Early Pliocene vertebrate fauna from Mallorca (Balearic Islands, Western Mediterranean): an update.’ Integrative Zoology. 9. pp.183-196. [Abstract only]

Bover, P., & Alcover, J. A. 2003. ‘Understanding Late Quaternary Extinctions: the case of Myotragus balearicus (Bate 1909).’ Journal of Biogeography. 30. pp. 771-781. [Abstract only]

Brown, P., et al. 2004. ‘A new small-bodied hominin from the Late Pleistocene of Flores, Indonesia.’ Nature. 431(7012). pp.1055-1061. [Full article]

Clauzon, G., et al. 1996. ‘Alternative interpretation of the Messinian salinity crisis: controversy resolved.’ Geology. 24. pp.363-366. [Full article]

Flynn, l., J., et al. 2013. ‘The Leporid Datum: a Late Miocene biotic marker.’ Mammal Review. 44(3-4). pp.164-176. [Full article]

Foster, J. B. 1964. ‘The evolution of mammals on islands.’ Nature. 202(4929). pp.234-235.

Ge, D., et al. 2013. ‘Evolutionary History of Lagomorphs in response to global environmental change.’ PLoS ONE. 8(4): doi.org/10.1371/journal.pone.0059668

Herridge, V. L., & Lister, A. M. 2012. ‘Extreme insular dwarfisms evolved in a mammoth.’ Proceedings of the Royal Society B: Biological Sciences. 279(4929). pp.234-235. [Full article]

Jalut, G., et al. 2000. ‘Holocene climatic changes in the Western Mediterranean, from south-east France to south-east Spain.’ Paleogeography, Paleoclimatology, Paleoecology. 160. pp.225-290. [Full article]

Manzi, V., et al. 2013. ‘Age refinement of the Messinian salinity crisis onset in the Mediterranean.’ Terra Nova. 25. pp. 315-327. [Full article]

Mas, G., et al., 2018. ‘Terrestrial colonisation of the Balearic Islands: new evidence for the Mediterranean sea-level drawdown during the Messinian Salinity Crisis.’ Geology. 46. pp.527-530. [Abstract only]

Quintana, J., et al. 2011. ‘Nuralagus rex, Gen. Et. Sp. Nov., An endemic insular giant rabbit from the Neogene of Minorca (Balearic Islands, Spain).’ Journal of Vertebrate Paleontology. 31(2). pp.231-240. [Full article]

Shindler, 2004. ‘Bate, Dorothea Minola Alice.’ Oxford Dictionary of National Biography. doi: https://doi.org/10.1093/ref:odnb/67163

Shindler, K. 2005. ‘Discovering Dorothea: the life of the pioneering fossil hunter Dorothea Bate.’ Harper Collins Publishers. [Book]

The Guardian 2019. True meaning of Watership Down revealed ahead of TV revival. [Online]

Posted in Mouse Goat, Nuralagus | Tagged , , , , , , , , , | 2 Comments

The Evolutionary History of Extinct and Living Lions

Posted on May 22, 2020 by twilightbeasts

I’m fairly obsessed with cave lions. If one were to open up my head and look at my brain’s RAM it would be something like 70% facts about extinct species of cat, 20% stuff that my wife and kids tell me to remember, 10% background processing needed to survive. As someone who has always been drawn to obscure knowledge, being one of the perhaps dozen or so people on the planet who has an in-depth appreciation of a species that went extinct 14,000 years ago deeply appeals to me.

Cave lions were magnificent apex predators that somehow managed to share the landscape with Eurasian peoples for three hundred centuries. During that time we painted them, we sculpted them, we hunted them, and were hunted by them in turn. They were as native to Europe as modern lions are to Africa and India. That’s the line I’ve taken in my book [shameless plug] The Missing Lynx, and learning about Pleistocene megafauna has forever changed the way I think about what is “natural”.

Our new paper in Proceedings of the National Academy of Sciences, PNAS (pronounced penis), is a massive collaborative effort that called on experts from the UK, USA, Spain, Denmark, China, Russia, Norway, Malaysia, Brazil, and Canada. The story starts way back in 2011. I was 31, with a 3 year old daughter and another on the way, and with friends in Copenhagen I used what little free time I still had left to write a Marie Curie grant application to look at the genomics of lions, with the idea of identifying genetic signals unique to the extinct North African Barbary lion. Project “Search for Innate Markers of Barbary Affinity”, or SIMBA for short, was envisioned as an international collaboration using my prior knowledge of lion genetics, the world-class facilities in Copenhagen for palaeogenomics, and the skills of experts in lion biology and genomic analysis to answer the question. Our collaborators had already assembled museum samples of lions from their complete natural range, including Pleistocene cave lions. I lived with my family in Copenhagen for two years with the sole aim of processing said lion samples and identifying the ones with the best preserved DNA to sequence more fully. At the end of that time we had produced genomic libraries from our best 14 samples: 1 cave lion from Siberia, 1 cave lion from the Yukon, 1 lion from Gabon, 1 lion from Sudan, 2 lions from Senegal, 1 lion from RSA, 2 extinct Cape lions, 3 extinct Barbary lions, 1 Iranian lion, and 1 Asian lion. For the first time we were able to use complete nuclear DNA, not just mitochondrial genomes to look at lion relationships. This was only supposed to be the first phase of Project SIMBA, with phase 2 being analysis of living zoo and menagerie individuals to screen for potential Barbary ancestry in the mix. As Barbary lions went extinct in the wild in the 1950s but were popular exhibits in even the first zoos of the post-medieval era, the possibility remains that some of our generic zoo lions could trace part of their ancestry back to North Africa. However, as things are wont to do, life got in the way of phase 2 of the project and it has taken nearly 9 years from start to finish of phase 1.

“Sultan” a Barbary lion in the New York Zoological Park in 1906. Public Domain Image.

A little bit of a detour into the nitty-gritty of actually “doing science”. It took months back in 2011 to put together the application case for why we should get funding and a 6-month wait to find out if we were successful. The money to fund this research for two years came from the European Union, before Brexit was anything more than a glint in Farage’s jaundiced eye. The ability to move freely from the UK to Denmark was crucial to this project, and can’t be overstated. This is the reality of doing science in the world today. It relies on international collaboration, free movement, and time to apply for funding. Getting money for research is insanely competitive and each year sees a drop in success rates. Many of the big sources of funding are only given to 5-10% of applicants. Each year, maybe 9 out of 10 grant applications are unsuccessful. Each one of these rejections represents the culmination of hundreds of hours of (usually unpaid) work and the dreams and aspirations of researchers who just want to do science. Even the successfully funded projects come with money for two or three years maximum work. Having to juggle doing the work you are paid (and desperately want) to do, while keeping an eye on the future is incredibly stressful. Most labs, even the great ones, are only one or two missed funding opportunities away from breaking up just from lack of money to cover their overheads. This was the case with my involvement in our study. After the requisite two years of funding I applied to a few funding agencies for more money for related projects with no success. I also applied for lecturing positions with the idea that teaching would still allow time to properly analyse and report on the data we had generated. From 2014 to 2017 I failed to secure anything that would fit the needs of our young family despite dozens of applications and a handful of interviews. In the meantime I took work delivering lecture content (on zero-hours contracts) at a university that declined to interview me for a permanent position teaching the same material. I worked for the excellent charity The Brilliant Club. I taught online courses for another university. I travelled 800km round trips to cover lectures at yet another university. Altogether trying to juggle the need to earn money, be the primary caregiver for our two children, and work on finishing SIMBA was just too much. Something had to give, and of course it was SIMBA and other academic work. It has taken a lot of personal reflection to come to terms with that decision. Despite this, since 2014 I’ve been an author on 24 peer-reviewed papers and reviews including 5 first author, and 2 last author works. I’ve not been idle!

All this is a long-winded way of saying I’ve found that working in science is hard, and many obstacles are put in the way for people that want to do it but have other responsibilities too. It’s taken me a lot of time and mental effort to reconcile this with my own needs and to make peace with the fact that for as long as academia continues to be an insecure career that requires its practitioners to uproot everything every 2-3 years, I don’t want to be part of it. I’m a good scientist, but a poor academic.

Back to the paper. My involvement consisted of countless hours in sterile clean rooms, suited and booted against contamination to extract and amplify DNA from museum samples and permafrost subfossils. The real meat of the work was done by collaborators who analysed the gigabase dataset of lion genomes I helped generate to test our assumptions about lion evolution. While I was flailing around outside of academia, joint first author Marc de Manuel really took the reins and steered the project towards completion. Collaborators in the USA and China gave invaluable access to present-day lion genomes and sequencing facilities to extend the reach of the study. In particular, access to high quality genomes from modern lions from India, Botswana, and Tanzania allowed us to anchor our samples to the surviving modern diversity.

Underneath all that PPE it really is me, about to work on some ancient lion DNA in the Copenhagen clean labs. Image © Ross Barnett

Our study’s conclusions are threefold. First of all we get a very detailed and precise handle on the timing of the separation of cave lions and the ancestors of modern lions. This appears to happen around about half a million years ago and tallies remarkably well with the fossil evidence and appearance of the ancestral cave lion (Panthera leo fossilis) in the bone records of Europe.

Secondly, we applied some pretty complex analyses to the question of whether there is evidence of cave lions and the ancestors of modern lions ever interbreeding. We know from detailed genomic analyses of the other big cats that hybridisation has been rife in the prehistoric past. Jaguar and lion. Lion and tiger. Snow leopard and lion. Mass hysteria!

So given that species with quite different behavioural cues had hybridised it made sense to look at whether cave lions and lions ever interbred after they split. Especially when there were known regions of potential overlap in southwestern Eurasia. Surprisingly, we didn’t find any evidence at all of hybridisation between cave lions and modern lions. This is in sharp contrast to the different lineages of modern lion that we identified. The deepest split, occurring 70,000 years ago, is between lions from West Africa, North Africa and Asia and those from the rest of Africa. This likely represents the influence of central rainforest expansion during the Pleistocene cutting off the west and north of the continent from the rest of the population since lions cannot hunt in densely forested areas. Within these lineages we found evidence of interbreeding: lions from central Africa show mixing between lions from northern African and southern African populations. More weirdly, Asian lions seem to show signs of having mixed with southern African lions. Perhaps as a result of now flooded connections along a southern dispersal route through the Arabian peninsula.

Thirdly, we get an excellent handle on diversity levels within different populations. We found the Indian lion to have incredibly low levels of genetic diversity, reflecting their long history of human persecution and a bottleneck to historic levels of <50 individuals within the past century. Interestingly, we don’t identify any signal of low diversity levels in either the extinct cave lion or extinct Barbary lion, suggesting that they were doing quite well before we came along.

Phylogeny of modern and ancient lions based on their nuclear genomes, showing separation between different lineages.

Thanks to the incredible analyses of my colleague Marc de Manuel and our coauthors we’ve managed to pull together the first paper that has genomes from not one but four different extinct lion groups: the cave lion, the middle eastern lion, the Cape lion, and the Barbary lion. I think I can stop thinking about lions for a while at least.

 

Written by Ross Barnett (@DeepFriedDNA)

Further Reading:

de Manuel, M., R. Barnett, M. Sandoval-Velasco, N. Yamaguchi, F. G. Vieira, M. L. Zepeda Mendoza, S. Liu, M. D. Martin, M. H. S. Sinding, S. S. T. Mak, C. Carøe, S. Liu, C. Guo, J. Zheng, G. Zazula, G. Baryshnikov, E. Eizirik, K. P. Koepfli, W. E. Johnson, A. Antunes, T. Sicheritz-Ponten, S. Gopalakrishnan, G. Larson, H. Yang, S. J. O’Brien, A. J. Hansen, G. Zhang, T. Marques-Bonet, and M. T. P. Gilbert. 2020. “The evolutionary history of extinct and living lions.” Proceedings of the National Academy of Sciences of the United States of America. [Full Text]

Posted in American Lion, Cave Lion, DNA, Homo sapiens | Tagged , , , , , , , , , , , , | 19 Comments