Tag: phylogeny

A possible Chinese ancestor for Denisovans, Neanderthals and modern humans

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Assigning human fossils older than around 250 ka to different groups of the genus Homo depends entirely on their physical features. That is because ancient DNA has yet to be found and analysed from specimens older than that. The phylogeny of older human remains is also generally restricted to the bones that make up their heads; 21 that are fixed together in the skull and face, plus the moveable lower jaw or mandible. Far more teeth than crania have been discovered and considerable weight is given to differences in human dentition. Teeth are not bones, but they are much more durable, having no fibrous structure and vary a great deal. The main problem for palaeoanthropologists is that living humans are very diverse in their cranial characteristics, and so it is reasonable to infer that all ancient human groups were characterised by such polymorphism, and may have overlapped in their physical appearance. A measure of this is that assigning fossils to anatomically modern humans, i.e. Homo sapiens, relies to a large extent on whether or not their lower mandible juts out to define a chin. All earlier hominins and indeed all other living apes might be regarded as ‘chinless wonders’! This pejorative term suggests dim-wittedness to most people, and anthropologists have had to inure themselves to such crude cultural conjecture.

The extraction, sequencing and comparison of ancient DNA from human fossils since 2010 has revealed that three distinct human species coexisted and interbred in Eurasia. Several well preserved examples of ancient Neanderthals and anatomically modern humans (AMH) have had their DNA sequenced, but a Denisovan genome has only emerged from a few bone fragments from the Denisova Cave in western Siberia. Whereas Neanderthals have well-known robust physical characters, until 2025 palaeoanthropologists had little idea of what Denisovans may have looked like. Then proteins and, most importantly, mitochondrial DNA (mtDNA) were extracted from a very robust skull found around 1931 in Harbin, China, dated at 146 ka. Analysis of the mtDNA and proteins, from dental plaque and bone respectively, reveal that the Harbin skull is likely to be that of a Denisovan. Previously it had been referred to as Homo longi, or ‘Dragon Man’, along with several other very robust Chinese skulls of a variety of ages.

The distorted Yunxian cranium (right) and its reconstruction (middle) [Credit: Guanghui Zhao] compared with the Harbin Denisovan cranium (left) [Hebei Geo University]

The sparse genetic data have been used to suggest the times when the three different coexisting groups diverged. DNA in Y chromosomes from Denisovans and Neanderthals suggest that the two lineages split from a common ancestor around 700 ka ago, whereas Neanderthals and modern humans diverged genetically at about 370 ka. Yet the presence of sections of DNA from both archaic groups in living humans and the discovery that a female Neanderthal from Denisova cave had a Neanderthal mother and a Denisovan father reveals that all three were interfertile when they met and interacted. Such admixture events clearly have implications for earlier humans. There are signs of at least 6 coexisting groups as far back as the Middle Pleistocene (781 to 126 ka), referred to by some as the ‘muddle in the middle’ because such an association has increasingly mystified palaeoanthropologists. A million-year-old, cranium found near Yunxian in Hubei Province, China, distorted by the pressure of sediments in which it was buried, has been digitally reconstructed.

This reconstruction encouraged a team of Chinese scientists, together with Chris Stringer of the UK Museum of Natural History, to undertake a complex statistical study of the Yunxian cranium. Their method compares it with anatomical data for all members of the genus Homo from Eurasia and Africa, i.e. as far back as the 2.4 Ma old H. habilis (Xiabo Feng and 12 others 2025. The phylogenetic position of the Yunxian cranium elucidates the origin of Homo longi and the Denisovans. Science, v. 389, p. 1320-1324; DOI: 10.1126/science.ado9202). The study has produced a plausible framework that suggests that the five large-brained humans known from 800 ka ago – Homo erectus (Asian), H. heidelbergensis, H. longi (Denisovans), H. sapiens, and H. neanderthalensis – began diverging from one another more than a million years ago. The authors regard the Yuxian specimen as an early participant in that evolutionary process. The fact that at least some remained interfertile long after the divergence began suggests that it was part of the earlier human evolutionary process. It is also possible that the repeated morphological divergence may stem from genetic drift. That process involves small populations with limited genetic diversity that are separated from other groups, perhaps by near-extinction in a population bottleneck or as a result of the founder effect when a small group splits from a larger population during migration. The global population of early humans was inevitably very low, and migrations would dilute and fragment each group’s gene pool.

The earliest evidence for migration of humans out of Africa emerged from the discovery of five 1.8 Ma old crania of H. erectus at Dmanisi to the east of the Black Sea in Georgia. similar archaic crania have been found in eastern Eurasia, especially China, at various localities with Early- to Middle Pleistocene dates. The earliest European large-brained humans – 1.2 to 0.8 Ma old H. antecessor from northern Spain – must have migrated a huge distance from either Africa or from eastern Eurasia and may have been a product of the divergence-convergence evolutionary framework suggested by Xiabo Feng and colleagues. Such a framework implies that even earlier members of what became the longi, heidelbergensis, neanderthalensis, and sapiens lineages may await either recognition or discovery elsewhere. But the whole issue raises questions about the widely held view that Homo sapiens first appeared 300 ka ago in North Africa and then populated the rest of that continent. Was that specimen a migrant from Eurasia or from elsewhere in Africa? The model suggested by Xiabo Feng and colleagues is already attracting controversy, but that is nothing new among palaeoanthropologists. Yet it is based on cutting edge phylogeny derived from physical characteristics of hominin fossils: the traditional approach by all palaeobiologists. Such disputes cannot be resolved without ancient DNA or protein assemblages. But neither is a completely hopeless task, for Siberian mammoth teeth have yielded DNA as old as 1.2 Ma and the record is held by genetic material recovered from sediments in Greenland that are up to 2.1 Ma old. The chances of pushing ancient human DNA studies back to the ‘muddle’ in the Middle Pleistocene depend on finding human fossils at high latitudes in sediments of past glacial maxima or very old permafrost, for DNA degrades more rapidly as environmental temperature rises.

See also: Natural History Museum press release. Analysis of reconstructed ancient skull pushes back our origins by 400,000 years to more than one million years ago. 25 September 2025; Bower, B. 2025. An ancient Chinese skull might change how we see our human roots. ScienceNews, 25 September 2025; Ghosh, P. 2025. Million-year-old skull rewrites human evolution, scientists claim. The Guardian, 25 September 2025

Was the earliest human ancestor a European?

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Charles Darwin famously suggested that humans evolved from apes, and since great apes (chimpanzees, bonobos and gorillas) live in Africa he reckoned it was probably there that the human ‘line’ began. Indeed, the mitochondrial DNA of chimpanzees (Pan troglodytes) is the closest to that of living humans. Palaeoanthropology in Africa has established evolutionary steps during the Pleistocene (2.0 to 0.3 Ma) by early members of the genus Homo: H. habilis, H. ergaster, H. erectus; H. heidelbergensis and the earliest H. sapiens. Members of the last three migrated to Eurasia, beginning around 1.8 Ma with the individuals found at Dmanisi in Georgia. The earliest African hominins emerged through the Late Miocene (7.0 to 5.3 Ma): Sahelanthropus tchadensi, Orrorin tugenensis and Ardipthecus kadabba. Through the Pliocene (5.3 to 2.9 Ma) and earliest Pleistocene two very distinct hominin groups appeared: the ‘gracile’ australopithecines (Ardipithecus ramidus; Australopithecus anamensis; Au. afarensis; Au. africanus; Au. sediba) and the ‘robust’ paranthropoids (Paranthropus aethiopicus; P. robustus and P. boisei). The last of the paranthropoids cohabited East Africa with early homo species until around 1.4 Ma. Most of these species have been covered in Earth-logs and an excellent time line of most hominin and early human fossils is hosted by Wikipedia.

All apes, including ourselves, and fossil examples are members of the Family Hominidae (hominids) which refers to the entire world. A Subfamily (Homininae) refers to African apes, with two Tribes. One, the Gorillini, refers to the two living species of gorilla. The other is the Hominini (hominins) that includes chimpanzees, living humans and all fossils believed to be on the evolutionary line to Homo. The Tribe Hominini is defined to have descended from the common ancestor of modern humans and chimps, and evolved only in Africa. As the definition of hominins stands, it excludes other possibilities! The Miocene of Africa before 7.2 Ma ‘goes cold’ as regards the evolution of hominins.  There are, however fossils of other African apes in earlier Miocene strata (8 to 18 Ma) that have been assigned to the Family Hominidae, i.e. hominids, of which more later.

Much has been made of using a ‘molecular clock’ to hint at the length of time since the mtDNA of living humans and chimps began to diverge from their last common ancestor. That is a crude measure at it depends entirely on assuming a fixed rate at which genetic mutation in primates take place. Many factors render it highly uncertain, until ancient DNA is recovered from times before about 400 ka, if ever. The approach suggests a range from 7 to 10 Ma, yet the evolutionary history of chimps based on fossils is practically invisible: the earliest fossil of a member of genus Pan is from the Middle Pleistocene (1.2 to 0.8 Ma) of Kenya. Indeed, we have little if any clue about what such a common ancestor looked like or did. So the course of human evolution relies entirely on the fossil sequence of earlier African hominins and comparing their physical appearances. Each species in the African time line displays two distinctive features. All were bipedal and had small canine teeth.  Modern chimps habitually use knuckle walking except when having to cross waterways. As with virtually all other primates, fossil or living, male chimps have large, threatening canines. In the absence of ancient DNA from fossils older than 0.4 Ma these two features present a practical if crude way of assessing to when and where the hominin time line leads.

In 2002 a Polish geologist on holiday at the beach at Trachilos on Crete discovered a trackway on a bedding plane in shallow-marine Miocene sediments. It had been left by what seems to have been a bipedal hominin. Subsequent research was able to date the footprints to about 6.05 Ma. Though younger than Sahelanthropus, the discovery potentially challenges the exclusivity of hominins to Africa. Unsurprisingly, publication of this tentative interpretation drew negative responses from some quarters. But the discovery helped resurrect the notion that Africa may have been colonised in the Miocene by hominins that had evolved in Europe. That had been hinted at by the 1872 excavation of Oreopithecus bambolii from an Upper Miocene (~7.6 Ma) lignite mine in Tuscany, Italy – a year after publication of Darwin’s The Descent of Man.

Lignites in Tuscany and Sardinia have since yielded many more specimens, so the species is well documented. Oreopithecus could walk on two legs, its hands were capable of a precision grip and it had relatively small canines. Its Wikipedia entry cautiously refers to it as ‘hominid’ – i.e. lumped with all apes to comply with current taxonomic theory (above). In 2019 another fascinating find was made in a clay pit in Bavaria, Germany. Danuvius guggenmosi lived 11.6 Ma ago and fossilised remains of its leg- and arm bones suggested that it could walk on two legs: it too may have been on the hominin line. But no remains of Danuvius’s skull or teeth have been found. There is now an embarrassment of riches as regards Miocene fossil apes from Europe and the Eastern Mediterranean (Sevim-Erol, A. and 8 others 2023. A new ape from Türkiye and the radiation of late Miocene hominines. Nature Communications Biology, v. 6, article  842.; DOI: 10.1038/s42003-023-05210-5). A number of them closely resemble the earliest fossil hominins of Africa, but most predate the hominin record there by several million years.

Phylogenetic links between fossils assigned to Hominidae found in Africa and north of the Mediterranean Sea. (Credit: Sevim-Erol et al. 2023, Fig 5)

Ayla Sevim-Erol of Ankara University, Turkiye and colleagues from Turkiye, Canada and the Netherlands describe a newly identified Miocene genus, Anadoluvius, which they place in the Subfamily Homininae dated to around 8.7 Ma. Fragments of crania and partial male and female mandibles from Anatolia show that its canines were small and comparable with those of younger African hominins, such as Ardipithecus and Australopithecus. But limb bones are yet to be found. Around the size of a large male chimpanzee, Anadoluvius lived in an ecosystem remarkably like the grasslands and dry forests of modern East Africa, with early species of giraffes, wart hogs, rhinos, diverse antelopes, zebras, elephants, porcupines, hyenas and lion-like carnivores. Sevim-Erol et al. have attempted to trace back hominin evolution further than is possible with African fossils. They compare various skeletal features of different fossils and living genera to assess varying degrees of similarity between each genus, applied to 23 genera. These comprised 7 hominids from the African Miocene, 2 early African hominins (Ardipithecus and Orrorin) and 10 Miocene hominids from Europe and the Eastern Mediterranean. They also assessed similarities with 4 living genera, Homo, orang utan (Pongo), gorilla and chimp (Pan).

The resulting phylogeny shows close morphological links within a cluster (green ‘pools’ on diagram) of non-African hominids with the African hominins, gorillas, humans and chimps. There are less-close relations between that cluster and the earlier Miocene hominids of Africa (blue ‘pool’) and the possible phylogeny of orang utans (orange ‘pool’). Sevim-Erol et al. note that African hominins are clearly more similar and perhaps more closely related to the fossils of Europe and the Eastern Mediterranean than they are to Miocene African hominids. This suggests that evolution among the non-African hominids ceased around the end of the Miocene Epoch north of the Mediterranean Sea. But it may have continued in Africa. Somehow, therefore, it became possible late in Miocene times for hominids to migrate from Europe to Africa. Yet the earlier, phylogenetically isolated African hominids seem to have ‘crashed’ at roughly the same time. Such a complex scenario cannot be supported by phylogenetic studies alone: it needs some kind of ecological impetus.

The Mediterranean Basin at the end of the Miocene Epoch when the only water was in the deepest parts of the basin. (Credit: Wikipedia, Creative Commons)

Following a ‘mild’ tectonic collision between the African continent and the Iberian Peninsula during the late Miocene connection between the Atlantic Ocean and the Mediterranean Sea was blocked from 6.0 to 5.3 Ma. Except for its deepest parts, seawater in the Mediterranean evaporated away to leave thick salt deposits. Rivers, such as the Rhône, Danube, Dneiper and Nile, shed sediments into the exposed basin. For 700 ka the basin was a fertile, sub-sea level plain, connecting Europe and North Africa over and E-W distance of 3860 km. There was little to stop the faunas of Eurasia and Africa migrating and intermingling, at a critical period in the evolution of the Family Hominidae. One genus presented with the opportunity was quite possibly the last common ancestor of all the hominins and chimps. The migratory window vanished at the end of the Miocene when what became the Strait of Gibraltar opened at 5.3 to allow Atlantic water. This resulted in the stupendous Zanclean flood with a flow rate about 1,000 times that of the present-day Amazon River. An animation of these events is worth watching