Friday, December 18, 2015

14 kya Archaic Hominin Remins Found In SW China

The number of Late Pleistocene hominin species and the timing of their extinction are issues receiving renewed attention following genomic evidence for interbreeding between the ancestors of some living humans and archaic taxa. Yet, major gaps in the fossil record and uncertainties surrounding the age of key fossils have meant that these questions remain poorly understood. 
Here we describe and compare a highly unusual femur from Late Pleistocene sediments at Maludong (Yunnan), Southwest China, recovered along with cranial remains that exhibit a mixture of anatomically modern human and archaic traits. Our studies show that the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora. However, the scarcity of later Middle and Late Pleistocene archaic remains in East Asia makes an assessment of systematically relevant character states difficult, warranting caution in assigning the specimen to a species at this time. The Maludong fossil probably samples an archaic population that survived until around 14,000 years ago in the biogeographically complex region of Southwest China.
Darren Curnoe et al., "A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China", PLoS ONE 10(12): e0143332 (December 18, 2005) (open access) via Dienekes' Anthropology Blog.

The site where the femur was found is better known as "Red Deer Cave" (which is what the Chinese name translates to). Another blog notes that:
Analysis of a 14,000 year-old partial human femur found in 1989 from the Maludong (Red Deer) Cave in the Yunnan, Southwest China states that the femur looks like that of early Homo erectus and H. habilis… Way more archaic in morphology than the dating implies. . . .
In 2012 the team published their analysis of the skull bones from the site. They speculated the bones could represent an unknown new species, or perhaps a very early and primitive-looking population of modern humans, which had migrated to the region more than 100,000 years ago. 
The thigh bone is more primitive than the skulls seem. The shaft is narrow and long with a thin cortex that is buttressed. This discovery is controversial because, until now, it had been thought that the youngest pre-modern humans on mainland Eurasia (Neanderthals and Denisovans) died out 40,000 years ago, soon after anatomically modern Homo sapiens entered the region. But… This find hints at the possibility a pre-modern species may have overlapped in time with modern humans on mainland East Asia.

Figure 2: Scatterplots comparing sample medians for subtrochanteric (ST) variables, neck-shaft angle and reconstructed body mass: (A) Anteroposterior (AP) diameter (mm). (B) Mediolateral (ML) diameter (mm). (C) Total area (TA: mm2). (D) Cortical area (CA: mm2). (E) %-Cortical area (%-CA). (F) Platymeric index (%). (G) Neck-shaft angle (°). (H) Reconstructed body mass (kg). (Error bars = 95% confidence interval of median [dark] and 1.5 x interquartile range [light]; Abbreviations: LPHO = Lower Pleistocene Homo; MPHO = Middle Pleistocene Homo; NEAN = Neanderthals; MPMH = Middle Pleistocene Modern Humans; EULU = Early Upper-Late Upper Palaeolithic.

Figure 4: Object plot from principal component analysis of 10 continuous variables: PC1 (52.85%) versus PC2 (28.92%) (AMH femora labeled in black; archaic hominins in blue; minimal spanning tree shown). [Ed. the new sample from 14,000 years ago is MLDG 1678 which shows clear affinity in the PCA chart to the archaic as opposed to the modern human femers.]

Figure 5. [Ed. The neighbor joining tree analysis likewise shows a strong affinity of the new sample to very archaic Homo Erectus femers.]

The opening of the paper notes (emphasis added) that:
The number of Late Pleistocene archaic hominin species, their biogeographical distribution, and the timing of their extinction remain important but intractable questions in palaeoanthropology. These issues have been brought into sharp relief over the last half-decade following the accumulation of genomic evidence for interbreeding between the Pleistocene ancestors of living humans and archaic hominins across much of the Old World. Yet, in many regions, archaic remains are sparse or absent from the Late Pleistocene fossil record. 
The few exceptions include: 1) the Neanderthals (H. neanderthalensis) in Europe, West Asia, and extending at times into southern Siberia, the youngest example being from Mezmaiskaya dating ~39 ka; 2) possibly the North African specimens Dar-es-Soltane and Témara from Morocco, with a reported age range of ~110 to 40–20 ka for the associated Aterian lithic industry; 3) fossils from Denisova Cave in southern Siberia consisting of a molar and manual and pedal phalanges that have been dated >50 ka, and whose phylogenetic position has been inferred from recovered genomic DNA sequences to be the sister species to the Neanderthals; 4) fragmentary cranial, mandibular and dental remains from Xujiayao in North China dating in the range of ~125–60 ka, and exhibiting a unique morphology including some similarities to Neanderthals; and 5) in Southeast Asia, H. floresiensis at Liang Bua Cave, Flores, dating ~74–17 ka, with its similarities to Lower Pleistocene and Pliocene hominins.

The dearth of Late Pleistocene archaic fossils makes the identification of a number of the species involved in episodes of interbreeding with early anatomically modern humans (AMH) problematic. One prominent example is the occurrence of “Denisovan” DNA in the genomes of some contemporary humans in East Asia and Australo-Melanesia suggesting their Pleistocene ancestors interbred with this anatomically poorly known taxon. While no fossils beyond Denisova Cave have been identified as belonging to this group, Denisovan mitochondrial diversity combined with the observed strong geographic patterning of Denisovan DNA in living people imply they were formerly widespread with a range extending perhaps into Southeast Asia.

Additionally, genomic research has shown that Neanderthals contributed more DNA to contemporary East Asians than Europeans indicating that multiple episodes of interbreeding must have occurred under a model of complex admixture and demographic scenarios across a wide geographic area. Yet, there is presently no direct evidence for their occupation of Asia anywhere east of the Altai Mountains. While some East Asian Middle Pleistocene remains like those from Maba in South China might show affinities to Neanderthals, they are probably too old to be related to the “classic” Neanderthals. Yet, other interpretations of the morphology of Chinese Middle Pleistocene fossils such as from Dali have proposed a role for gene flow between archaic hominins and AMH in the emergence of recent East Asian populations.

Pinpointing the extinction date for archaic hominins is also important for understanding the adaptive and demographic responses of these species to the arrival of AMH beyond rare interbreeding events. As hominins fit the definition of megafauna, the circumstances surrounding their extinction also potentially adds to understanding of the impacts AMH had on the environment during the Late Pleistocene and their potential role in the demise of a wide range of large-bodied mammal species. 
Several of the current authors have previously reported the occurrence of hominin cranial remains from two sites in Southwest China (Maludong and Longlin or Laomaocao Cave) that combine archaic hominin and AMH traits. In the case of the unusual cranium from Longlin Cave, it was recently concluded that its mosaic morphology probably results from hybridisation between AMH and an unknown archaic species, perhaps even occurring during the early Holocene. A similar explanation might also apply to the morphology of the Maludong cranial fossils, a hypothesis currently under investigation by us.

Here we report a partial proximal femur from Maludong (Yunnan), Southwest China, found in association with these unusual cranial remains, which shows morphological and phylogenetic affinities to archaic hominins. The Maludong hominins were all recovered from sediments dated with AMS 14C of charcoal to between about 14,310±340 cal. yr BP and 13,590±160 cal. yr BP. Thus, the Maludong femur is the youngest fossil with archaic morphology found to date and potentially extends the overlap of AMH and archaic hominins in East Asia to >50 ka.
The individual probably weighed about 110 pounds (50 kilograms).

The paper closes with these remarks:
Putting the results of our analyses together, MLDG 1678 shows morphological and phylogenetic affinities to archaic femora, particularly Lower Pleistocene early Homo. We conclude, therefore, that the Maludong femur represents an individual that probably belonged to an archaic taxon rather than AMH. Just which taxon it represents is difficult to determine, however, because of the scarcity of Late Pleistocene hominin femora from East Asia. It also remains unclear whether Late Pleistocene archaic groups from western Eurasia provide the most appropriate model for East Asian hominins during this period. In the case of AMH, though, we did include femora from East Asia, including the four from Minatogawa, and MLDG 1678 was found to be very distinct from them.

It is intriguing that such a plesiomorphic hominin could have survived at Maludong until near the end of the Pleistocene. Yet, this finding applies also to H. floresiensis, with its apparent minimum geological age only slightly older than MLDG 1678. Homo floresiensis has only been found on the island of Flores in eastern Indonesia though, and its occurrence has been explained by island biogeography. Moreover, the Maludong femur is distinct from the highly unusual femora of this species, with its unique mosaic of traits including resemblances to Australopithecus taxa. One possible explanation is that the Maludong femur samples the population presently known only from Denisova Cave in the Altai region and dubbed the “Denisovans”. Another candidate is the presently unnamed taxon represented by the Xujiayao fossils. However, the absence of femora from both of these groups makes these scenarios impossible to test at present. Besides, the similarities of MLDG 1678 to Lower Pleistocene
hominins implies that other possibilities should be considered, such as a late surviving descendent of a Lower Pleistocene East Asian group or even the Dmanisi hominins.

Yunnan Province is characterised by complex topography associated with Himalayan uplift and extrusion of the Indochina block resulting in vicarious biogeographic divisions. It is one of 20 floristic endemic centres in China, comprising subtropical evergreen broad-leaved and sclerophyllous forests, and contains high levels of palaeoendemism. The region around Maludong is also biogeographically on the northern edge of tropical Southeast Asia. Thus, the Maludong femur might represent a relic, tropically adapted, archaic population that survived relatively late in the biogeographically complex region of Southwest China.

These remains appear to be archaic hominins, or at least hybrids of modern humans and hominins with high levels of archaic admixture which are dated to a time period 30,000 more years after we would have any reason to suspect their existence.  Unless these individuals were Denisovans or modern human-Denisovan hybrids, there is no trace of archaic hominin admixture from such a species in modern humans in East Asia or elsewhere.

The simplest explanation would be that while Homo Erectus was almost wiped out almost everywhere ca. 100,000-50,000 year ago, that a relict population survived but admixed with modern humans shortly after their arrival (or upon a later first contact with modern humans) in South China, and that this relict population survived but did not expand meaningfully for tens of thousands of years after all other Homo Erectus went extinct, before this population too went extinct in the Mesolithic era or early Holocene era, perhaps because the adoption of farming and herding by modern humans during the Neolithic Revolution in China tipped the balance such that modern humans wiped out these hybrid Homo Erectus individuals.

Of course, yet another possibility is that the dating or the analysis assigning these features to archaic genetic admixture are flawed in some respect or another.  Since the claim that this find seems to support is so extraordinary, the proof that must support it for it to be accepted as accurate must also be extraordinary.

Background: Modern Humans Outside Africa

It is undisputed that modern humans has entered crossed the Wallace line into places like Flores, Papua New Guinea, and Australia, probably from India via Southeast Asia, by 55,000 years ago, and there is one set of modern human remains in mainland Southeast Asia dated to around 65,000 years ago, but not very definitively.  There is strong, although not completely incontrovertible evidence, that the same group of modern humans were present in India continuously both before and after the massive volcanic Toba eruption that took place ca. 75,000 years ago.

The earliest signs of modern humans outside of Africa, in the form of tools and other relics, are in Arabia, date to ca. 120,000 years ago and show affinities to a modern human archaeological culture in Nubia.  The earliest remains that appear to be modern human outside of Africa are from Israel and date to about 100,000 years ago.  But, conventional wisdom holds that this population represents either an Out of Africa migration that failed, or one that did not significantly expand, until much later.

There are several cases in which bones that appear to be modern human from Southern China have been dated to 100,000 years ago or more, despite the fact that conventional wisdom would not expect any modern human remains in Southern China until about 73,000 years ago (a couple of thousand years after the Toba eruption which seems to have cleared the way for modern humans to enter Southeast Asia and East Asia via a Southern route).  There are a small number of remains and relics associated with Homo Erectus in Southeast Asia and East Asia up to about 100,000 years ago.

Conventional wisdom had been that the overlap was due to bad dating, and the older of the 100,000+ year old modern human finds in South China were tainted with poor archaeological methodology and the specter that there was pressure to bend the data to support the Chinese Communist government's favored "multi-regional evolution" theory (which is mostly not true, although archaic admixture has modestly complicated a pure Out of Africa theory of modern human evolution).

But, the lack of archaic Homo Erectus admixture in mainland Southeast and East Asia, and the lack of significant overlap between the period in which remains and relics associated with Homo Erectus and remains and relics associated with modern humans are found in Southeast Asia and East Asia, until now has strongly supported the inference that the complete extinction of Homo Erectus (apart of Homo Florensis if they are related) accompanied the appearance of modern humans in Southeast Asia and East Asia.

Of course, the low levels of non-Neanderthal archaic admixture in mainland Southeast Asia and East Asia could instead be due to a high level of dilution of first wave modern human populations by later waves of migrants to mainland Southeast Asia and East Asia after archaic hominins were extinct or moribund in the region.  Indeed, this dilution almost certainly did take place, although the extent to which modern humans in Southeast Asia and East Asia are derived genetically from the first wave of migrations is hard to assess with any great accuracy.

Given the near total absence of data, it is also possible that Denisovans rather than modern humans, caused the extinction of Homo Erectus and may have even briefly replaced Homo Erectus before modern humans became predominant in Southeast Asia and East Asia, and simply did not leave any remains or relics that Asian archaeologists have found yet.

Background: A Brief Summary of Archaic Hominin Archaeology

Hominins evolved in Africa in a complex several million year story through many intermediate species, some of which coexisted in Africa at the same time, and others of which ended up going extinct without leaving descendant species.

Modern humans derive (in Africa ca. 250,000 years ago) from a species that evolved from Homo Erectus, a species evolves in Africa ca. 2,000,000 years ago that is also a remote ancestor of Neanderthals and probably all other non-African hominins.

The Lower Pleistocene era, begins around the time that Homo Erectus evolves.  Homo Erectus expands into Africa around 1.8 million years ago (the type fossil for Homo Erectus is from the island of Java around 1.8 million years ago).  The Lower Pleistocene era ends around the time that Neanderthals emerge, a few hundred thousand years ago.  There is no convincing evidence of further significant evolution of Homo Erectus once it reaches Asia, although the evidence isn't rich enough to confirm or deny this hypothesis either.

The Middle Pleistocene era is basically the time period during which Neanderthals thrived in Eurasia from the Atlantic in the West, to Central Europe and Southern Siberia in the North, to India in the East, to Levant and Arabia in the South.  As discussed more later, all modern humans outside Africa have low levels of Neanderthal admixture and a recent ancient DNA find from Ethiopia concluded that most Africans also have lower levels of Neanderthal admixture probably from relatively recent admixture with non-African modern humans.

In Southeast Asia and East Asia during the Middle Pleistocene era, Homo Erectus was the dominant hominin species, while Neanderthals reigned in Europe and modern humans were starting to emerge in Africa.  Southeast Asia and East Asia area also has less advanced stone tools than are found in areas where Neanderthals were present.

A few hundred thousand years before the Neanderthals evolved, there is a European hominin species known as Homo Heidelbergus which evolved from Homo Erectus.  It was once widely assumed that Homo Heidelbergus was ancestral to Neanderthals, but recent ancient DNA evidence has cast doubt on this conventional wisdom.  The true story probably isn't that simple.

The youngest archaic hominin remains, other than Homo Florensis (a.k.a. Hobbit) remains on the island of Flores, anywhere east of India are about 100,000 years old.  Neanderthals go extinct around 29,000 years ago in Southeast Europe or West Asia.  Neanderthals and modern humans co-existed in Europe from about 42,000 years ago to 29,000 years ago, although not nearly so long in any one place.  Neanderthals and modern humans co-existed earlier than that in SW Asia and West Asia (and perhaps India or part of India and Central Asia as well).

We have good whole genome data from a handful of bones of a hominin called Denisovans, after the cave where the ancient DNA was found, which were a sister clade of Neanderthals genetically.  But, vexingly, we have too little data to reconstruct a skeleton of one or to even make much sense of their material culture and hunting habits.

Substantial Denisovan admixture is present thousands of miles away from Southern Siberia where this ancient DNA was found in aboriginal Australians and Papuans, lower levels are found in Negrito populations in the Philippines, and trace levels are found in East Asia, Tibet, the Americas, mainland Southeast Asia, and island Southeast Asia (although it is absent in India, the Andaman Islands and West Eurasia).  Denisovans could be a highly derived species of late Eurasian Homo Erectus, a derived species of Neanderthals or their ancestor, or could be related to Homo Heidelbergus, or could be a hybrid of some of these, or could be some previously unattested hominin species that is none of the above.

The Denisovan DNA shows what are arguably traces of both Neanderthal and Homo Erectus admixture (with much more of the former than the latter).  If this conclusion is correct, than Denisovans could not themselves have been Homo Erectus and the genetic evidence tends to point to a much more recent origin for this hominin species than the 2 million years that we would expect for Homo Erectus.

Homo Florensis is probably either a subspecies of Homo Erectus that experience island dwarfism, or a representative of the Denisovans (with or without island dwarfism), or a hybrid of the two, or both, or some entirely different kind of hominin species.  No ancient Homo Florensis DNA has been successfully obtained.

We have statistical traces of recent low levels of admixture with unidentified archaic hominins in the population genetics of a couple of African populations.

Background: The Genetic Evidence

Genetic evidence (including recent ancient DNA evidence that can use non-mutation rate methods to determine the time of the most recent Neanderthal admixture of the ancestors of a Paleolithic modern human in Northern Europe) points to ages for the most basal Y-DNA and mtDNA haplogroups that are ancestral to all non-African modern humans, and to Neanderthal admixture which is shared by all non-African modern humans in roughly similar amounts to sometime on the order of 75,000 to 50,000 years ago, at the dawn of the Upper Paleolithic era, or the tail end of the Middle Paleolithic era (a.k.a. the Middle Pleistocene).


Y-DNA haplogroups A, B and E are predominantly African in distribution and likely originate there.

All predominantly non-African Y-DNA haplogroups except Y-DNA haplogroups C and D are derived from Y-DNA haplogroup F, which most likely expands from a center of expansion in India. Y-DNA C likely also expanded from India to the East, although it is sometimes found at low frequencies in ancient European DNA.  Y-DNA C and F have a deep common ancestor in Y-DNA CF.

Y-DNA D has an odd distribution. It is found in trace frequencies in West Africans (where the haplogroup that is the common ancestor of Y-DNA haplogroups D and E called Y-DNA DE* is also found), is predominant among indigenous Andamanese Islanders, is found at moderate frequencies among the people of Tibet (where Y-DNA DE* is also found), is found at low to moderate frequencies in various Paleo-North Asian populations, and is found at a high frequency of a highly diverged branch of Y-DNA D in Japan.  Thus, Y-DNA D may indicate either a relict of an early Northern route migration by modern humans, or a maritime expansion that eventually worked its way inland to relatively unpopulated areas.


All non-African mtDNA haplogroups derive from the most basal forms of mtDNA M and N which is sister clades to various other clades of mtDNA L3 which is a predominantly African mtDNA haplogroup.  mtDNA M has a predominantly Asian distribution quite similar to Y-DNA haplogroup C except for mtDNA M1 which has a predominantly North African and East African overlapping heavily with certain haplogroups of Y-DNA E and the Afro-Asiatic linguistic area that almost surely represented an Upper Paloelithic back migration of modern humans to Africa (and coincides with time depth with the probably separate back migration of mtDNA U6 to Africa).


Chris Davies said...

"Y-DNA D has an odd distribution. It is found in trace frequencies in West Africans (where the haplogroup that is the common ancestor of Y-DNA haplogroups D and E called Y-DNA DE* is also found),.."

I would like to see any references for this. I am aware of DE* presence in West Africa along with the many different clades of E..but never heard of 'D' itself turning up there.

capra internetensis said...

Thanks for the extensive review.

I second the question, D in Africa? There was a recent paper that listed D instead of DE* in a table but that seems to have been a typo.

andrew said...

I'll have to look at that when I have a moment. I was writing from memory but memory can get faulty when you start to get gray hair in your beard.