Showing posts with label Eurasia. Show all posts
Showing posts with label Eurasia. Show all posts

Thursday, 18 June 2026

An alternative hypothesis on the origin of Hominins and African Apes.

The ancestors of Humans are commonly thought to have evolved on the savannas of Africa, a theory which was originally proposed by Charles Darwin. This original proposition was based upon the fact that our closest ancestors, the African Apes, lived in the forests of Africa, and that our upright walking behaviour seemed like an adaption to open grasslands, rather than any fossil evidence available at the time. This is a plausible hypothesis, and much subsequent palaeoarchaeological evidence uncovered in Africa has appeared to support it. However, a number of recent discoveries have been hard to reconcile with this scenario, leading to the emergence of alternative ideas on Human origins.

There are a number of things about Human anatomy which appear to be inconsistent with an origin on the African Savannas. We have a furless body, a layer of subcutaneous white fat, feet much flatter than other primates, run slowly, and sweat heavily when hot or exercising, leading to the loss of fluids and minerals (our water consumption needs are high compared to other Primates even when not doing this).

For a long time it was hypothesised that knuckle-walking African forest Apes migrated onto the open grasslands, where they evolved into upright Australophithecenes, and subsequently into Humans. Over time, this theory has been modified as we have come to understand more about the environments favoured by Australopithecenes, they are now seen as inhabitants of mosaic woodlands who moved from a partially bipedal lifestyle to an obligate bipedal one to facilitate crossing more open areas, although why this should be the case remains unclear.

Another puzzle is the apparent absence of fossils ascribed to either the genera Pan (Chimpanzees) or Gorilla, despite the long lineage of fossil Human-ancestors dating back into the Pliocene. The genera Australopithecus, Paranthropus, Sahelanthropus, Orrorin, and Ardipithecus, have all been classified as Hominins, more closely related to modern Humans than either Pan or Gorilla. This is in contradiction to what would be expected, as genetic studies suggest modern Chimpanzee and Gorilla populations have diverged from large ancestral populations, while Humans apparently descend from a lineage with consistently small population sizes and repeated genetic bottlenecks. It has been suggested that this has come about because the ancestors of Chimpanzees and Gorillas lived in acidic forests, where there is lower potential for remains to become fossilised. However, this environment is more favoured by Orangutans, which do have a fossil record, than it is by Chimpanzees, which do not.

'Mrs Ples' a 2.1 million-year-old skull assigned to the species Australopithecus africanus in the collection of the Ditsong National Museum of Natural History. José Braga/Didier Descouens/Wikimedia Commons.

In a review article published in the journal Academia Biology on 10 June 2026, Marc Verhaegen of the Anthropology Study Center in Putte, Belgium, Stephen Munro of the National Museum of Australia, Kathelijne Bonne of GondwanaTalks in Madrid, Spain, Frances Mansfield, an independent researcher from Volos in Greece, and Mario Vaneechoutte of the Faculty of Medicine and Health Sciences at Ghent University, present a new hypothesis on the origins of both Humans and African Apes, in which they argue that the Australopithecenes were not, in fact the ancestors of Humans but rather of modern Gorillas and Chimpanzees. 

Verhaegen et al. not that genomic studies have found that the ancestors of modern Gorillas and Chimpanzees were infected with the Endoretroviruses PtERV1 (CERV1) and PtERV2 (CERV2) between 3 and 4 million years ago (Endoretroviruses are fragments of ancient viral DNA which have been inserted into the hosts genome), but Humans and Asian Apes show no signs of any such infections in their past. Since Humans are not immune to the effects of these Viruses, the most likely explanation is that our ancestors were geographically isolated from the epidemic. It has been suggested that Human ancestors may have moved out of Africa during much of the Miocene Epoch, when the Viruses were circulating, but Verhaegen et al. suggest that a more likely scenario is that they did not arrive in Africa at all until the Early Pleistocene. Few, if any, Animals are thought to have migrated from Africa to Europe during the Pliocene, while a range of European Animals migrated into Africa, driven by the hyper-arid climate that emerged in southern Europe at this time. 

Furthermore, Verhaegen et al. consider that the Australopithecines found in Africa during the Pliocene were not closely related to modern Humans, but rather that their smaller brains, short legs, and long arms indicate that they were related, or even ancestral, to modern African Apes. The evolution of Australopithecenes has often been seen as confusing, as earlier species often have more Human-like traits, seen as 'advanced', while later forms are often more Ape-like, or 'primitive', leading to speculation about undiscovered ghost lineages connecting earlier species to Humans. 

This distinction vanishes if Australopithecines are considered to be the ancestors of African Apes. For example, the Miocene Ardipithecus ramidus, which lived about 4.4 million years ago, had small canine teeth, similar to those seen in modern Humans, whereas the Pliocene Australopithecus africanus had much larger canines, comparable to a modern Ape. Other examples are the Miocene Orrorin tugenensis, which lived about 6 million years ago, had femurs more closely resembling those of Humans that any Pliocene Australopithecene, and the Early Pliocene Australopithecus anamensis, which lived about 4.2 million years ago, had a modified talar trochlea which would have enabled it to swing its leg forward during upright locomotion, something which is absent in subsequent members of the genus. Furthermore, later Austalopithecenes such as the Early Pleistocene Australopithecus sediba, which lived about 1.8 million years ago, appear better adapted to an arboreal lifestyle than earlier members of the group.

A cast of a skull of Ardipithecus ramidus from the Miocene of Ethiopia, in the collection of the Royal Tyrrell Museum. Chris Woodrich/Wikimedia Commons.

Other than an early adaptation to bipedalism, Verhaegen et al. see Australopithecenes as consistently more Ape-like than they are Human-like, in particular noting that Australopithecus afarensis appears more Gorilla-like and Australopithecus africanus appears more Chimpanzee-like.

Verhaegen et al. do not see Homo habilis, the smallest and earliest member of the genus Homo, which appeared in the Early Pleistocene, about 2.58 million years ago, to be a true member of the genus Homo, noting that the species shares a small brain, short leg, and long arm morphology with Australopithecenes and Apes, and in particular that the morphology of the enamel–dentine junction in this species is also more Australopithecene-like. The later, but equally small, Homo naledi is also considered to be an Australopithecene. 

In Verhaegen et al.'s view, the last common ancestor of all Australopithecenes, living Apes, and Humans, would have been an upright Miocene Ape, capable of bipedal locomotion, climbing trees, and wading in shallow water. They describe a scenario in which these Apes led a lifestyle they describe as 'aquaborealism', living in forests which were at least seasonally flooded, with a lifestyle which involved wading in waters on the forest floor, climbing trees in a vertical position, and swinging beneath branches (branchiating). From this ancestral state the Hyobatids (Gibbons and Siamangs) evolved into small, fast branchiating Apes living in the tree canopy, Orangutans into larger, slower, branchiating forms, Gorillas and Chimpanzees (separately) into knuckle-walking forms, and Humans into bipedal walkers.

They give two potential scenarios from which modern African Apes could descend from Australopithecenes; either Chimpanzees descended directly from earlier, more gracile Australopithecenes, such as Australopithecus afarensis and Australopithecus africanus, while Gorillas arose from later, more robust forms such as Paranthropus boisei and Paranthropus robustus, or they went through separate but parallel evolutionary paths, running something like Australopithecus africanus-Paranthropus robustus-Chimpanzees and Australopithecus afarensis-Paranthropus boisei-Gorillas, in response to similar environmental changes.

A skull reconstruction assigned to Paranthropus robustus in the collection of the National Natural History Museum of China. Erlend Bjørtvedt/Wikimedia Commons.

Verhaegen et al. believe that the view of the common ancestor of Apes and Humans as being Ape-like, and Apes therefore as the 'primitive' state, has distorted our view of Hominid evolution for over a century. They argue that while Australopithecenes do have some Human-like traits, these are indicators that Australopithecenes are ancestral to Humans, but rather that they share some traits derived from a mutual common ancestor that frequently adopted an upright bipedal posture as an adaptation to life in flooded forests. 

The analysis presented by Verhaegen et al. suggests two distinct phases of Human evolution associated with wet environments; an initial aquaboreal phase in flooded Miocene forests, followed by a littoral (beach dwelling) phase, which may have involved frequent shallow diving to access food, which probably continued into the Early Pleistocene.

Apes differ from Old World Monkeys in a number of ways, the most obvious of which is their much larger size. This appears likely to have been a trait found in the last common ancestor of all Apes; even the relatively small Hylobatids are thought to have evolved from a larger ancestor, due to their long gestation period, which is unusual in such a small Primate, and is thought to be a hangover from a larger ancestor. Another notable trait is the absence of a tail in Apes. This has become much reduced, and forms a part of the 'pelvic cup'; a modification of the pelvis which helps to support the intestines when in an upright position. There is no comparable tail loss in any other Primate to which this can be compared, but the idea that this was an adaptation to an upright posture while engaged in vertical climbing and branchiating seems reasonable. Furthermore, if these ancestral Apes were spending a lot of time in wading in water, then a tail might have been disadvantageous, prone to heat loss, adding to the friction of the Apes when moving through the water, and prone to infections or attacks by predators. 

Verhaegen et al. note that quadruped Animals returning to the water tend to evolve in one of two ways. Those that use spinal flexation as the main means of propulsion and the tail as the driving organ, such as Whales and Sirenians, tend to lose their hind limbs, whereas those that use their limbs for propulsion, such as Seals, Bears, Penguins, and Hippos, tend to lose their tails. An exception can be seen in Animals such as Otters and Beavers, which use their tails for propulsion but make extensive use of their limbs for foraging and movement on land. Apes, which use their limbs to swim when they enter the water, have lost their tails.

The lumbar spine of Apes is stiffer and further from their dorsal surface than is the case in most Mammals, and their forelimbs (arms) are notably long, adaptations which seems favourable to climbing in an upright position and hanging below branches. They also have wide hips compared to other Primates, and a flatter pelvis, facilitating lateral leg movements, as well as a broader sternum and thorax, which pushes their scapulas into a more dorsal position, facilitating lateral and upward arm movements. 

Fossils of Miocene Apes are often found in what have been interpreted as warm, wet, forest environments, which has led to the suggestion that they may have been aquaborreal in nature, spending their time wading through flooded forests or climbing in the branches above with their arms. Such behaviour is known in extant Apes, for example Gorillas have been observed entering forest swamps to forage for Sedges, Bonobos will wade through water to obtain Waterlilies, and Orangutans have been observed wading in shallow water in Borneo.

Bipedal Gorilla, wading. Female Gorilla with a walking stick, while crossing bipedally an Elephant pool at Mbeli Bai, Republic of Congo. Thomas Breuer & Emma Stokes in Verhaegen et al. (2011).

Verhaegen et al. propose that all modern Apes derived from this initial aquaboreal Miocene Ape, with Gibbons adopting a fast branchiating motion, Orangutans a slower branchiating movement combined with knuckle walking, Gorillas and Chimpanzees separately developing a knuckle walking gait, and the ancestors of Humans going through a distinct litoral (coast dwelling) phase.

A number of lines of evidence have pointed towards Early Pleistocene members of the genus Homo may have engaged in regular wading, swimming, and even diving. Homo erectus has been observed to have a pachyosteoscletotic skeleton (i.e. unusually dense bones), something associated with slow-moving, shallow-diving Tetrapods such as Sireneans, as well as the earliest Whales and Seals. The dense skeleton can help such Animals maintain their position in the water, particularly in saltwater environments (where the body is more buoyant). The occipital bones of Homo erectus are roughly twice as thick as those of comparably sized Apes, making the interpretation of the species as a swift bipedal predator chasing down prey hard to sustain. 

Furthermore, the low positioning of the braincase, receding forehead, absence of a chin, and forward projecting face of Homo eructus appear to be an adaptation to frequent shallow water diving, and possibly floating on their backs. The forward pointing face and paranasal sinuses of Homo eructus may indicate a habit of surfacing nose first, with the nostrils above water and the heavy occipital area at the back of the head beneath the water, something which would have worked well in a back-floating position. The basicranial flexation of modern Humans holds our face in a ventral, forward facing position. In contrast, Homo erectus would have tended to look upwards, in what would be a forward position when swimming or diving (Neanderthals are somewhere between these positions). This has been suggested to be an adaptation to foraging in coastal waters, where the easy availability of coastal food sources would compensate for the lack of stability associated with a bipedal gait on land.

Several skulls of Homo erectus have been shown to have bony growths in the inner ear called aural exotoses (or surfer's ear) which is caused by chronic exposure to cold water. This has also been observed in about half of all Neanderthals. Verhaegen et al. observe that this directly contradicts the frequent claim that there is no direct palaeontological support for the coastal Ape hypothesis.

At the same time, Human-ancestors underwent both an increase in both overall body size, and relative brain size. This is a common adaptation to moving from a terrestrial to an aquatic lifestyle, seen for example in Whales and Dolphins, but is not typical when non-aquatic Mammals increase in size; for example, the largest Apes, Gorillas, do not have relatively large brains. Homo erectus underwent a significant increase in brain size, with later specimens had a brain twice as large as that of an equivalent-sized Ape. This may have benefited from the higher proportion of nutrients such as docosahexaenoic acid, folic acid, selenium, taurine, and iodine, in aquatic-derived foods, all of which are needed for brain-growth. Such disproportionate brain growth is not seen in terrestrial carnivores, and therefore seems unlikely in a Hominin chasing prey in open grassland. Notably, Australopithicenes never showed any notable increase in brain size over their two-million-year history. Verhaegen et al. take this as evidence that early Homo did not evolve from such ancestors on the African grasslands, since there seems no good reason that our brains should have started to grow rapidly while remaining in the same environment.

There is also considerable evidence that Homo erectus did consume aquatic foods. Fossils of Homo erectus from Mojokerto on Java were found in association with numerous marine Bivalve shells, while those at Trinil on the same island, were found with the shells of  freshwater Bivalves, such as Pseudodon and Elongaria, including specimens engraved with geometric patterns. Furthermore, palaeoarchaeological remains from the Koobi Fora Formation in the Turkana Basin of northern Kenya have yielded stone tools from a Oldowan technology alongside the remains of aquatic Animals including Fish, Turtles, and even Crocodiles. Early Homo specimens from a variety of locations have dental wear associated with grit and the oral processing of marine Molluscs. Archaic members of the genus Homo are known to have reached Sulawesi by one million years ago, despite this island never being connected to the Eurasian mainland, suggesting an early ability to cross open water.

A Pseudodon shell with geometric engravings from the Trinil archaeological site in East Java, dated to about 500 000 years ago. The shell was excavated by Dutch palaeoarchaeologist Eugène Dubois in the 1880s and taken to the Netherlands. It was returned to Indonesia by the Naturalis Biodiversity Center in 2025. Naturalis Biodiversity Center/Wikimedia Commons.

The genus Homo first appeared around the beginning of the Pleistocene, with the first evidence of the consumption of aquatic foodstuffs appearing about two million years ago, across the tropical and temperate regions of the Old World. This has led to the suggestion that Homo was able to spread across this area rapidly by following coasts and rivers, wading and diving for food. There is also increasing evidence for the consumption of aquatic foods by Neanderthals across their range, as well as Modern Humans across the world, and from their earliest appearance. 

Humans differentiate from the standard morphology and physiology of Primates, and indeed terrestrial Mammals in general, in several ways. We have fleshy outward lips, a small oral opening, a closed tooth row, a more globular tongue, a descended larynx, and an external nose that still today some individuals can partially close, using nasal muscles. We also have a distinct 'Cupid's bow' to our upper lips (technically the philtrum) to our upper lips, another feature which some modern individuals can use to close their nasal airway. All of these are adaptations which enable us to regulate breathing and seal our airways better, and which may have been more pronounced in Homo erectus.

Feeding on shellfish would also have required adaptations which required improved abilities to control the sucking and swallowing of food, particularly if this was done in the water. Adaptations which improved fine control over the lips, jaw, tongue, glottis, and larynx, would also have acted as pre-adaptations for the later evolution of speech. Hunting for foodstuffs underwater, particularly if we were doing this blind (by touch alone) is also likely to have improved both our manual dexterity and the sense of touch in our fingers, something also seen in Raccoons and Otters.

In Humans, the connective tissues, tendons, ligaments, and muscles of the human foot are aligned with the hallux to form a longitudinal arch. This is unlike the foot of any other Primate, and is a good adaption to walking, and acts as a shock-absorber when running. However, it is also a particularly good adaptation to swimming, particularly as our feet are relatively larger and more paddle-shaped, and makes us particularly sure-footed on wet or infirm terrain, where other Mammals often struggle. Humans are able to swim using axial undulation, a coordinated wave of motion from trunk to hips to legs, something other Primates are unable to do. Our feet can be seen as a trade-off between something useful for swimming and something useful on land. Notably, we are less efficient runners than most other Mammals, which directly contradicts the idea that we evolved to chase large prey across grasslands.

Notably, Humans have a layer of white fat beneath our skins (the adipose layer) considerably thicker than found in any other Primate, as well as an overall fat content which is also distinctively high. In a healthy male Human, between 12% and 23% of the body mass is fat, while in a female it is between 25% and 35%. In Chimpanzees and Bonobos body fat typically makes up less than 5% of the body mass of males, and less than 8% of the bodymass of females. Thus even the leanest of Humans have a significantly higher proportion of fat than healthy Chimpanzees. This suggests that Humans have undergone a significant ecological shift after our ancestors split from those of Chimpanzees, and one which decoupled the fat content of our bodies from the its use as an energy store. Such a change is again typical of aquatic and semi-aquatic Mammals, where fat has an important role both as an insulator and as a buoyancy aid. Such a layer provides no particular role during activities such as sustained running, and may be disadvantageous, as it can hamper the dissipation of heat.

Verhaegen et al. believe that plate tectonics played an important role in the evolution of Hominoids, Hominids, and Hominins, and in particular the formation of the Red Sea and the African Rift. Until about 30 million years ago (Early Oligocene), Africa and Arabia were a single island continent, separated from Eurasia by the Tethys Ocean. Over time, this continent drifted northward, the Tethys Ocean narrowed, and a series of islands and archipelagos formed between the two continents.

Between about 30 million years ago and about 20 million years ago (during the Oligocene and Early Miocene), an episode of plume volcanism beneath the Afar Triangle led to uplift, basalt volcanism, and the formation of a triple junction rift system. The three branches of this rift would go on to form the Gulf of Aden to the east, the Red Sea to the northwest, and the Ethiopian Rift to the south. At this time Eurasia and Africa-Arabia were still separated, although the Mesopotamian Seaway, which separated Arabia from what would become Mesopotamia and Persia, was becoming increasingly narrow.

Between about 20 million years ago and about 14 million years ago (Early-Middle Miocene) the Mesopotamian Seaway slowly closed, leading to the formation of a connection called the Gomphotherium Landbridge (Gomphotherium being a type of early Elephant that migrated out of Africa across this landbridge), leading to faunal exchange between Africa-Arabia to the south and Eurasia to the north. forming the first wave of the 'Great Old World Biotic Interchange', while the Mediterranean Sea and Indian Ocean became isolated from one-another. This also led to uplift and mountain formation along the Bitlis-Zagros Suture Zone, and the development of the Dead Sea Transform and Aqaba faults in response to the added tectonic stress. At this time the Red Sea had opened, and was connected to the Mediterranean by by the Gulf of Suez, but a land bridge at Bab-al-Mandeb, connecting Arabia to Africa, separated it from the Gulf of Aden.

Between about 14 million years ago and about six million years ago (Late Miocene), movement on the Dead Sea Transform Fault, combined with the mass of sediments around the Nile Delta, closed off the connection between the Red Sea and the Mediterranean at the Gulf of Suez. Following this, the Red Sea underwent a desiccation crisis, drying up and leaving vast salt deposits, albeit with occasional marine incursions.

Between about 5.9 and 5.33 million years ago (latest Miocene), the Gulf of Gibraltar also closed, cutting off the inflow of water from the Atlantic to the Mediterranean, and triggering the Messinian Salinity Crisis, in which the Mediterranean largely dried up, leaving a vast and inhospitable salt plain. 

After about 5.33 million years ago (Pliocene), the straits of Bab-al-Mandeb opened up allowing the Red Sea to flood from the Gulf of Aden, and the Strait of Gibraltar reopened, allowing the Mediterranean to refill from the Atlantic (the Zanclean Megaflood). Around this time the Gulf of Suez reconnected to the Mediterranean, cutting off Africa from the Red Sea until the beginning of the Pleistocene, when a land bridge formed across the Sinai again.

Simplified tectonic and palaeogeographic evolution of the Mediterranean Sea and the Arabian Peninsula, with key marine connections between Africa, Arabia, and Eurasia (details of European and Paratethys geographies not given). (1) Before 30 million years ago (until the Rupelian, Oligocene); (2) 30–20 million years ago (Rupelian–Burdigalian); (3) 20–14 million years ago (Burdigalian–Langhian); (4) 14–6 million years ago; (5) From about 5.9 to 5.33 million years ago: the Strait of Gibraltar closed due to plate tectonics; (6) From 5.33 million years ago onwards. Red circle in (2): Afar plume basalt eruptions; brown line in (3): uplifting mountain front at the Bitlis-Zagros Suture Zone; red line in (3) and (4): active Dead Sea Transform Fault; pale orange in (4) and (5): desiccated marine domains; blue arrows in (6): marine gateways and direction of filling of basins. Verhaegen et al. (2026).

Verhaegen et al. suggest two alternative scenarios for the emergence of the first Apes. One scenario sees a group of Early Miocene Primates living in coastal forests and islands along the Mesopotamian Seaway, which gave rise to both the Apes and the Old World Monkeys. The other sees these ancestors living in coastal forests in East Africa, which migrated northward along the Red Sea Rift as it opened, migrating into the Arabian Peninsula and then eventually into Eurasia. This latter scenario is supported by the presence of the possible Ape Morotopithecus in Uganda about 20.6 million years ago, although the exact status of this fossil is unclear.

In either scenario, Early Apes increased in size rapidly after splitting from the Old World Monkeys, at the same time developing a very broad and strong sternum in a broad thorax, a somewhat shorter lumbar spine with only five lower and more centrally placed lumbar vertebrae (indicative of a vertical body posture), an enlarged sacrum equipped with a coccyx in a broad pelvis (cup form, supporting the intestines), external tail loss, relatively longer legs (indicative of wading), and longer arms (indicative of below-branch hanging). These early Apes are thought to have lived in (probably coastal) swamp forests, hanging beneath branches, practising aquarbourism, and developing to an upright bipedal stance. 

These early Apes probably spread along the northern coast of the Tethys Ocean, with different groups splitting off and going their own way, beginning with the Gibbons. Between 22.4 and 16 million years ago the ancestors of the Orangutans had split from those of the African Apes, moving eastward towards the coastal forests of Southeast Asia, while the proto-African Apes colonised forests along the Western Tethys (what would become the Mediterranean). 

There is a surprising absence of Ape or Hominid fossils from the Middle Miocene of Africa (between about 13 and 10 million years ago). At the same time, Eurasia has an abundance of both, particularly in southern Europe and Anatolia, with many forms looking like plausible ancestors for African Apes. Verhaegen et al. cite this as support for the idea that the ancestors of modern Humans and African Apes were not in Africa during this time, but instead in southwestern Eurasia. At this time much of southern Europe was covered by  inland seas, mega-lakes, swamps, and coastal forests, and home to Dryopithecine Apes such as Dryopithecus, Pierolapithecus, Danuvius, and Rudapithecus, which are potentially ancestral to modern Gorillas, Chimpanzees, and Humans.

A partial skull of Pierolapithecus catalaunicus, a Dryopithecine Ape from the Middle Miocene of Spain. Institut Català de Paleontologia Miquel Crusafont.

During the Vallesian Crisis (between about 11.6 and 8.7 million years ago) the climate of southern Europe became much drier and the extensive forests shrank, being replaced by open grasslands. Many of the Apes there died out, while surviving forms, such as Ouranopithecus and Graecopithecus adapted to the new environment by becoming more bipedal, and foraging in mixed woodlands and river valleys. These Apes could potentially be ancestral to later Australopithecenes and African Ape (one Turkish Ape from this period, Anadoluvius turkae, has been suggested as an offshoot from the line which led to Gorillas).

The scenario envisaged by Verhaegen et al. has a group of Dryopithecine Apes taking advantage of the closure of the Mesopotamian Sea, and migrating to the swamp forests surrounding the early Red Sea. The ancestors of Orangutans must have split from these western Apes before 14 million years ago, when the Badenian Transgression would have blocked migration between Europe and East Asia. The lineage which led to Gorillas probably split off next, migrating from Europe, where taxa such as Ouranopithecus remained, while closer ancestors such as Anadoluvius turkae migrated through Anatolia, and on to Africa, where they gave rise to Gorilla-like African Apes such as Chororapithecus and Sahelanthropus, then eventually the East African Australopithecenes and modern Gorillas.

At the same time, Graecopithecus and similar species around the Mediterranean could provide plausible ancestors for Chimpanzees and Humans, explaining the Hominid-like footprints seen at Trachilos on Crete about six millions of years ago (long before the earliest such footprints in Africa). The lineage which led to Humans and Chimpanzees must also have migrated southward, at latest during the onset of the Messinian Salinity Crisis about 5.9 million years ago, which would have made the Mediterranean Basin uninhabitable. The route from Europe into Africa across the Sinai Peninsula would have been cut off during the Zanclean Megaflood (5.33 million years ago), which filled the Mediterranean and over-spilled into the Red Sea, filling that too. The final connection between Arabia and Africa was lost about 5 million years ago, when the Bab-el-Mandeb Strait opened, connecting the Red Sea to the Gulf of Aden.

Verhaegen et al. suggest that some of these Apes crossed into Africa before 5 million years ago, giving rise to the Southern African Australopithecines and eventually modern Chimpanzees. Another group remained on the southern shore of Arabia, where they were forced to turn increasingly to the littoral environment for survival, as the land became increasingly arid and hostile.

Around 2.8 million years ago the Earth's climate cooled sharply, leading sealevels to drop abruptly. At this time early Homo migrated from Arabia into Africa and Eurasia, leading to the sudden appearance of Homo erectus across the Old World. 

A reconstruction of the skull of Homo erectus in the collection of the University of Michigan Museum of Natural History. Thomas Roche/Wikimedia Commons.

Under this scenario, the genus Homo is absent from Africa until the Early Pleistocene appearance of Homo erectus/Homo eregastor, with the Pliocene Australopithecines not being ancestral to Modern Humans, but instead relatives of Chimpanzees and Gorillas. This view is broadly in-line with several recent cladistic analyses of Human origins, which suggest African Apes and Humans are derived from Eurasian Apes, and that there were multiple crossings from Eurasia into Africa. 

Verhaegen et al. take the view that East and Southern African Australopitecines largely evolved in parallel, in response to similar ecological pressures. Thus the gracile forms, Australopithecus afarensis and Australopithecus africanus, appeared in the Pliocene, when they were able to live in forest, and in particular swamp forest, environments, whereas the more robust Early Pleistocene forms, Paranthropus boisei and Paranthropus robustus, evolved in response to cooler, drier conditions, although generally sticking close to large bodies of water, such as Papyrus swamps. Eventually the modern African Apes adopted to a life on dry forest floors.

It is possible that the Southern African Australopithecines were more omnivorous, whereas the East African forms adapted to the processing of tougher plant materials, something which is reflected in the diets of modern Chimpanzees and Gorillas. 

This later arrival of Human-ancestors into Africa provides an explanation for the absence of any trace of the Endoretroviruses PtERV1 (CERV1) and PtERV2 (CERV2) in our genomes, while the ancestors of Gorillas and Chimpanzees were affected. The potential littoral phase also explains the many morphological adaptations which set Humans apart from other Apes, as well as behavioural traits such as a fondness for water and sea coasts. 

Verhaegen et al. believe that the earliest members of the genus Homo were shelfish divers, something which would have provided them with the resources for accelerated brain growth, as well as adaptions such as an external nose and pachyosteosclerotic skeleton. As supporting evidence for this, they cite the frequent occurrence of ear exostoses (surfer's ear) in early Homo, as well as tooth wear associated with a shellfish diet, the early arrival of Homo on remote islands such as Flores and Sulawesi, and the co-occurrence of their fossils and tools with shells, and even engraved shells.

See also...

Sunday, 7 May 2023

Human DNA extracted from a Palaeolithic pendant.

Understanding the changes in technology and population that went on during the Palaeolithic is the key to understanding much of the history of our species. Unfortunately, Palaeolithic deposits tend to be highly condensed, so that objects and remains found alongside one-another may be separated by hundreds or even thousands and years, making it impossible to connect artefacts to remains unless they were clearly directly buried together. 

Recent advances in the recovery of DNA from ancient sediments provide us with the possibility of establish connections between artefacts and specific Human populations, although this would require the recovery of DNA directly from the objects in question. Potentially, artefacts made from tooth and bone have the best chance of preserving ancient DNA, as they are porous and capable of absorbing body fluids, and because they contain hydroxyapatite, which is known to both absorb and preserve DNA. Thus ancient pieces of tooth or bone may potentially preserve DNA not only from the Animal from which they came, but also DNA from other organisms that came into contact with them after that Animal's death, For the most part, this tends to be the DNA of Microorganisms which colonised the decaying body of the original Animal, but could also potentially include Humans which handled these pieces, or made things from them. 

However, Palaeolithic artefacts made from tooth and bone are extremely rare, and therefore of great value to science, something particularly true of pendants or other objects likely to have been worn close to the skin for long periods of time, and therefore the most likely to have absorbed ancient Human DNA. The conservation of such objects is therefore considered a high priority, and archaeologists are reluctant to expose them to the destructive methods used to extract DNA, or even to soak them in buffers which might absorb DNA passively, as these can alter specimens irreparably. 

In a paper published in the journal Nature on 3 May 2023, a team of scientists led by Elena Essel of the Max Planck Institute for Evolutionary Anthropology, Elena Zavala, also of the Max Planck Institute for Evolutionary Anthropology, and of the Department of Biology at San Francisco State University, and the Department of Molecular and Cell Biology at the University of California, Berkeley, Ellen Schulz-Kornas of the Department of Cariology, Endodontology and Periodontology at the University of Leipzig, Marie Soressi of the Faculty of Archaeology at Leiden University, and Matthias Meyer, again of the Max Planck Institute for Evolutionary Anthropology, describe development of a method for non-destructively recovering DNA from ancient bone and tooth artefacts, and the first results obtained using this technique.

In order to test potential reagents for DNA extraction from ancient artefacts, Essel et al. first obtained ten pieces of faunal remains from the  Quinçay and Les Cottés Palaeolithic sites in France, none of which are thought to have been deliberately modified by Human activity, but all of which were similar in size and shape to common bone and tooth artefacts. These were immersed in ten different potential reagents, including a guanidinium thiocyanate-containing reagent previously suggested for non-destructive DNA extraction, an ethylenediaminetetraacetate (EDTA) solution, which is a decalcifier commonly used in ancient DNA extraction,  a sodium hypochlorite (bleach) solution, which is an oxidizing reagent used to remove surface-exposed contaminant DNA, and a sodium phosphate buffer supplemented with detergent, which has been recently shown to enable temperature-controlled DNA release from powdered bone samples.

The microtopography of the surface of these artefacts was mapped  using quantitative 3D surface texture analysis prior to immersion, and then again once the samples were removed, in order to detect any changes caused by the reagents. The guanidinium thiocyanate-containing reagent and ethylenediaminetetraacetate solution were both found to cause significant alteration to the samples, whereas all of the other samples caused much smaller and more sporadic changes (none of the reagents caused zero alterations), possibly due to the removal of small particles of soil and other substances from the sample surfaces. 

Faunal remains used in reagent testing. Photographs of samples taken before and after treatment with various reagents used in ancient DNA extraction (GuSCN, guanidine thiocyanate reagent; EDTA, ethylenediaminetetraacetate solution; Phosphate, sodium phosphate buffer with detergent; Bleach, sodium hypochlorite solution). The black bar represents 1 cm. Note that colours are not directly comparable, as the photographs were taken at slightly different angles, with different light settings and camera adjustments. Essel et al. (2023).

Based upon this, Essel et al. were able to develop a step-wise method for the extraction of DNA from ancient bone and tooth artefacts. using serial incubations in sodium phosphate buffer at 21, 37, 60 and 90 °C, with three incubations per temperature.

Workflow of the gradual, non-destructive DNA extraction method using sodium phosphate buffer at elevated temperatures. Essel et al. (2023).

Next Essel et al. applied this to eleven bone and tooth objects from Châtelperronian layers of Quinçay Cave in France, all of which are believed to have potentially been used as tools between 35 000 and 45 000 years ago. One of these objects (Q10), identified as a piece of Reindeer bone, yielded 1828 fragments of Cervid mitochondrial DNA, which showed elevated frequencies of cytosine-to-thymine substitutions at their ends, which is consistent with the deamination of cytosine seen in other ancient DNA samples, and which has been used to date such DNA. Another object (Q15), identified as a piece of ivory, yielded 2004 fragments of Elephantid mitochondrial DNA, again showing cytosine-to-thymine substitutions. All eleven samples also yielded Hominid and Suid mitochondrial DNA, none of which showed cytosine-to-thymine substitutions, and all of which is therefore is considered to be the result of modern contamination. Since all of these samples were found several decades ago, and were neither collected or stored under sterile conditions, this was not surprising.

Artefacts before and after DNA extraction. Photographs of samples taken before and after phosphate-based, non-destructive DNA extraction. The black bar represents 1 cm. Note that colors are not directly comparable, as the photographs were taken at slightly different angles, with different light settings and camera adjustments. Essel et al. (2023).

Given that contamination by modern DNA appeared to be ubiquitous in ancient bone and tooth objects that had been handled by hand, Essel et al. decided to directly obtain objects from ongoing excavations at two Palaeolithic sites currently still under investigation; Bacho Kiro Cave in Bulgaria, and Denisova Cave in the Altai Republic of southern Siberia. Three tooth pendants (‘BKP1–BKP3) were obtained from Bacho Kiro, and one (DCP1) from Denisova Cave, all by archaeologists wearing gloves and facemasks to prevent contamination.

Photograph of DCP1 as it became exposed during excavation. The photograph was taken shortly before the pendant was removed and placed into a plastic bag using gloves. Essel et al. (2023).

Large and visible chunks of soil were removed from these artifacts by (gloved) hand, and they were washed in water three times before being subjected to the phosphate buffer DNA extraction technique. All four pendants produced ancient Mammalian mitochondrial DNA, with BKP1 producing Bovid DNA, BKP2 and BKP3 producing Ursid DNA, and DCP1 producing Cervid DNA. Human mitochondrial DNA was recovered at much lower levels than from the Quinçay material, and very few pieces of Suid DNA suggesting that the modified excavation method had helped prevent the contamination of these samples. Notably, the DCP1 Human mitochondrial DNA showed signs of significant cytosine deamination, suggesting that this was indeed ancient Human DNA.

Photographs of DCP1 before and after cleaning and non-destructive DNA extraction. Essel et al. (2023).

Very little ancient Human mitochondrial DNA was recovered from the Bacho Kiro Cave material, with the largest sample, 29 deaminated fragments, coming from a soil particle attached to BKP3. In contrast, DCP1 produced significant amounts of ancient Human mitochondrial DNA, enabling the construction of a near-complete consensus sequence, which could be used to place the material within a phylogenetic analysis. This DNA seemed to mostly (but not exclusively) originate from a single individual, assigned to mitochondrial haplogroup U (because mitochondrial DNA is found in the mitochondria, organelles outside the cell nucleus, it is passed directly from mother to child without being sexually recombined each generation, enabling precise estimations of when individuals shared common ancestors, at least through the female line, forming a mitochondrial  haplogroup).

Essel et al. estimate that this Human mitochondrial DNA came from an individual lived about 18 500 years ago, and falls within a group of Ancient North Eurasians who otherwise are known from further east within Siberia, including the 24 000-year-old Mal’ta 1 individual, and the 17 000-year-old Afontova Gora 3 individuals. All of these samples are more closely related to one-another than to modern North Eurasians, and show affinities to other ancient Siberians and Native Americans. As well as the mitochondrial DNA, sufficient chromosomal DNA was recovered to establish that the individual was female.

Essel et al.'s work establishes that it is possible to recover ancient Human DNA from bone and tooth artefacts, providing a previously unexplored source of information about the makers and users of these ancient objects. The amount of ancient DNA recovered from DCP1 was comparable to that obtained from well-preserved Pleistocene Human remains, and the recovery of both Human and Cervid DNA from the same object enabled two separate cytosine deamination dates from the same artefact.

Future work will determine how frequently such ancient Human DNA is preserved within bone and took artefacts. Essel et al. recommend that all archaeologists working with such material adopt the practice of wearing gloves and masks while extracting bone and tooth sample at archaeological sites, and express the hope that in future it might be possible to establish a dataset which can connect specific late Pleistocene technologies to specific ancient Human populations.

See also...

Follow Sciency Thoughts on Facebook.

Follow Sciency Thoughts on Twitter.


Thursday, 6 August 2015

Cryptic diversity: A new species of Wolf from Africa.


Cryptic species are species which closely resemble other species and which can only be separated by careful anatomical examination or even genetic analysis. In recent years the widespread application of DNA analysis to populations of wild animals  has led to the discovery that many well-known species are in fact clusters of cryptic species, with profound implications for the conservation of these species; a single large widespread population suddenly becoming a number of smaller more localized populations. 

Golden Jackals, Canis aureus, from North Africa have long been noted for being larger and more robust than Jackals from either Sub-Saharan Africa or Eurasia, leading to speculation that they may represent a separate species or sub-species. A study published in 2011 in the journal PLoS One based upon analysis of mitochondrial DNA found that Jackals from Egypt and Ethiopia were in fact not Jackals at all, but were more closely related to the Grey Wolf, Canis lupus, and suggested that these should be described as a separate subspecies of Wolf, the African Wolf, Canis lupus lupaster. A follow-up study published in the same journal in 2012 found that the mitochondrial lineage ascribed to Canis lupus lupaster was also present in Canids in West Africa, among animals considered to be more typically Jackal-like.

In a paper published in the journal Current Biology on 17 August 2015, a team of biologists led by Klaus-Peter Koepfli of the Smithsonian Conservation Biology Institute and the Theodosius Dobzhansky Center for Genome Bioinformatics at St. Petersburg State University and John Pollinger of the Department of Ecology and Evolutionary Biology at the University of California, Los Angeles publish the results of a much wider study of mitochondrial and nuclear DNA from populations of Golden Jackals from across Southern Europe and the Middle East, as well as Israel, Morocco, Algeria, Mauritania, Senegal and Kenya, and discusses these results and their implications for the classification of African Jackals.

All of the African Jackals were found to be a separate species from the Eurasian Jackals, and more closely related to the Eurasian Grey Wolf. However these African Wolves appear to have separated from their Eurasian cousins over a million years ago, and were judges sufficiently genetically distinct to be placed in a separate species. Examination of taxonomic records for Canids revealed that the French biologist Cuvier had described a ‘Jackal’ from Senegal as a separate species, Canis anthus, in 1820, an analysis that was rejected by subsequent biologists who failed to spot any significant morphological difference between African and Eurasian Jackals. For this reason Koepfli & Pollinger et al. suggest that African Golden Jackals henceforth be referred to as African Golden Wolves, Canis anthus, rejecting Canis lupus lupaster as a valid name.

Phylogenetic Tree Based on Mitochondrial Cytochrome b Sequences and Sampling Localities of Golden Jackals Used in This Study (A) Maximum-likelihood phylogram of 104 cytochrome b sequences (1,140 bp). Haplotype number is shown next to taxon name and locality. Accession numbers indicate sequences downloaded from GenBank. Haplotypes without accession numbers are novel sequences generated for the present study. Asterisks at nodes indicate bootstrap support R80% based on maximum-likelihood analyses (500 pseudoreplicates) and R0.95 posterior probability from Bayesian inference. Canis spp. from Egypt are indicated by thick arrows. Haplotypes labeled as Canis lupus lupaster refer to the African wolf. The tree was rooted using Sechuran Fox (Lycalopex sechurae) as outgroup. Scale bar indicates the number of substitutions per site. Photo credits: left, Golden Jackal from Senegal (CIBIO/Monia Nakamura); centre, Mexican Gray Wolf (Tom and Pat Leeson); right, Golden Jackal from Israel (Eyal Cohen). (B) Map of geographic localities showing where Golden Jackals were sampled. Relative number of animals sampled from each locality is shown. Hatched lines indicates geographic range of Golden Jackal based on International Union for the Conservation of Nature distribution. Koepfli & Pollinger et al. (2015).

Morphologically the African Golden Wolf and Eurasian Golden Jackal are very hard to tell apart, other than the distinct largeness of the North African specimens; the African Wolf was, on average slightly broader in the snout than the Eurasian Jackal, but not distinctively enough for this to be used as a reliable feature to distinguish the species.

The Golden Jackal samples from Israel were found to be mostly hybrid animals, containing DNA from Eurasian Golden Jackals, Grey Wolves, African Golden Wolves and Dogs. Two Golden Wolves from Egypt were found to have mitochondrial DNA (which is passed through the female line without recombination) from Eurasian Jackals and Grey Wolves, suggesting that hybridization was occurring here too, though whole genome analysis of Egyptian samples was not carried out.

Comparison of the genomes of African Golden Wolves and Dogs suggest that a small amount of Dog DNA derives from African, rather than Grey Wolves; this is roughly comparable to the amount of Neanderthal DNA found in modern Humans, with two groups of Dogs, the Basanji (African Laughing Dog) and Dingo, having higher levels of Golden Wolf DNA than other groups.

This scenario suggests that Africa has repeatedly been invaded by different Canid lineages from Eurasia. Koepfli & Pollinger et al. suggest that this relates to the changeable climate of the Pleistocene Era, with warmer wetter periods when it was possible for Canids to move between Eurasia and Africa, and cooler dryer periods when these populations became reproductively isolated.

See also…

Morphometric analysis is a method used by palaeontologists to sort bones and shells into taxonomic and ecological groups. It relies...


Foxes (Vulpini) are a subgroup of the Dog Family, Canidae, found in North America, Eurasia and Africa (South American Foxes are a separate group, more closely related to True Dogs than to other Foxes). The...


Dogs are our oldest domestic animal, and the only one which predates the adoption of agriculture. This has led to a great deal of study of the origin of domestic dogs over the years. Despite this we are still not entirely sure where dogs were first domesticated. We are now confident that domestic dogs are descended from a...



Follow Sciency Thoughts on Facebook.

Friday, 12 September 2014

Magnitude 1.9 Earthquake in North Yorkshire.

The British Geological Survey recorded a Magnitude 1.9 Earthquake at a depth of 1 km in southern North Yorkshire slightly after 11.30 pm British Summertime (sightly after 10.30 pm GMT) on Thursday 11 September 2014. This is quite a small quake, and there was no danger of it causing any damage or injuries, but it people have reported feeling it in parts of North and East Yorkshire.

The approximate location of the 11 September 2014 North Yorkshire Earthquake. Google Maps.

Earthquakes become more common as you travel north and west in Great Britain, with the west coast of Scotland being the most quake-prone part of the island and the northwest of Wales being more prone  to quakes than the rest of Wales or most of England.

The precise cause of Earthquakes in the UK can be hard to determine; the country is not close to any obvious single cause of such activity such as a plate margin, but is subject to tectonic pressures from several different sources, with most quakes probably being the result of the interplay between these forces.

Britain is being pushed to the east by the expansion of the Atlantic Ocean and to the north by the impact of Africa into Europe from the south. It is also affected by lesser areas of tectonic spreading beneath the North Sea, Rhine Valley and Bay of Biscay. Finally the country is subject to glacial rebound; until about 10 000 years ago much of the north of the country was covered by a thick layer of glacial ice (this is believed to have been thickest on the west coast of Scotland), pushing the rocks of the British lithosphere down into the underlying mantle. This ice is now gone, and the rocks are springing (slowly) back into their original position, causing the occasional Earthquake in the process. 

(Top) Simplified diagram showing principle of glacial rebound. Wikipedia. (Bottom) Map showing the rate of glacial rebound in various parts of the UK. Note that some parts of England and Wales show negative values, these areas are being pushed down slightly by uplift in Scotland, as the entire landmass is quite rigid and acts a bit like a see-saw. Climate North East.

Witness accounts of Earthquakes can help geologists to understand these events, and the structures that cause them. If you felt this quake, or were in the area but did not (which is also useful information) then you can report it to the British Geological Survey here.

See also...


The British Geological Survey recorded a Magnitude 1.7 Earthquake at a depth of 1 km, roughly 5 km to the west...


A Magnitude 1.9 Earthquake occurred at a depth of about 1 km roughly 10 km to the east of Doncaster in South Yorkshire, slightly after 4.50 am British...



On Wednesday 23 May at about 10.45 pm British Summertime (11.45 GMT), the British Geological Survey recorded an Earthquake in South Yourkshire, roughly 3 km west of the Village of Thorne, or 10 northeast of Doncaster, measuring 1.4 on the Richter Scale and at a depth of 1 km. This is a very small quake and is highly unlikely to have caused any damage or injuries, but may have been felt as it was close to the surface.




Follow Sciency Thoughts on Facebook.