Archaic Hominins Crossed The Wallace Line Long Ago

Stone tools dated with related animals remains show that archaic hominins had crossed the Wallace line by 1.26 ± 0.22  million years ago. 

Presumably, these archaic hominins would have been Homo erectus although there are no associated hominin bones past the Wallace line to confirm that this was the case.

Razib Khan on Denisovans

Razib Khan does a good job of summing up some of the things that we've learned in recent years about Denisovans, an archaic hominin clade.

[I]n June 2025, Chinese paleogeneticist Qiaomei Fu published data finally connecting specific fossil remains to Denisovans, utilizing both mtDNA and protein sequencing methods. And so now we know that Denisovans and Homo longi, are one and the same. A rather well preserved fossil from Harbin, China, a nearly complete skull, first identified as a new species in a 2021 publication, and colloquially dubbed Dragon Man, turns out to have DNA that we can now see neatly matches the sequences extracted from Denisova cave. For fifteen years, the label Denisovan only applied in a genomic context. No longer. Denisovan physical remains were in fact in plain sight all along.

This is not entirely a surprise. Some geneticists and paleoanthropologists have long assumed that many among the wealth of the fossils languishing yet to be identified, catalogued or named in East Asian collections today were Denisovans (I said as much in a podcast with Vagheesh Narasimhan of UT Austin, when H. longi was announced four years ago). Also, since 2010, we have established that Denisovans are the ancestors of more than Papuans and other Australasians. The Negrito peoples of the Philippines have a substantial contribution from Denisovans, the same as their Papuan neighbors from New Guinea to the south. But when you set aside their majority Austronesian ancestry (a much more recent overlay), it appears their forager ancestors (today some 35% of their ancestry) carried even more Denisovan ancestry than Papuans, on the order of 7-8%. It is also clear that low, but detectable, levels of Denisovan ancestry appear today in populations across South, East and Southeast Asia, at fractions of 0.1-0.3%.

 

Partial skull of Homo longi, AKA a Denisovan

The attested presence of Denisovan ancestry across a vast triangle stretching from Pakistan to Japan to Australia argues that they were present across vast territories. Deeper analysis of the Denisovan fragments in the genomes of Asians, Melanesians and Australians suggest at minimum two admixture events with two very distinct Denisovan populations. One population is clearly related to the genomes we have from Denisova cave. These northern Denisovans mixed with the ancestors of modern East Asians. But the Denisovan ancestry in South and Southeast Asians, as well as in Melanesians and Australians, is clearly from a population with a distinct ancestry; likely one that split off from the northern subspecies as long as more than 350,000 years ago. And the plot thickens, because tentative evidence gleaned from comparing the segments carried by these populations with southern Denisovan ancestry suggests distinct admixtures here as well; one in South Asians, another in Southeast Asians (a common one with Melanesians and Australians), and perhaps even one or two further ones in the outer reaches of prehistoric Sundaland and Sahul.

Population Replacement In The Columbian Highlands

In Europe, the first farmers of Europe, derived from Western Anatolian farmers, largely replaced Europe's original hunter-gatherers (who actually show continuity between the periods before and immediately after the Last Glacial Maximum), and in turn, received very substantial genetic admixture from late Copper Age/early Bronze Age Indo-Europeans from more or less where Ukraine is today. This diluted both first farmer ancestry, and the already highly diluted European hunter-gather ancestry that was admixed into those first farmer populations. In some places, like Britain, the population replacement of first farmers by Indo-Europeans was nearly complete.

Something similar apparently happened in East and Southeast Asia.

A new study established that the Americas did not break from this pattern, with some of its early agriculturists replacing pre-existing hunter-gatherer populations in a similarly genocidal pattern. If anything, this replacement was even more complete.

Sometime between 4000 BCE and 0 CE, in the Columbian highlands, probably coinciding with a new archaeological culture whose artifacts appear around 1000 BCE to 800 BCE, a millennium after maize cultivation began around 1800 BCE (but possibly before the full blown ceramic culture emerged), a clade of indigenous South American hunter-gatherers (with ancestry dating back to the initial wave of human settlement of South America) were replaced by a different group of indigenous South Americans.

The 1800 BCE date is from A. Gómez, et al., "A Holocene pollen record of vegetation change and human impact from Pantano de Vargas, an intra-Andean basin of Duitama, Colombia." 145 Rev. Palaeobot. Palynol. 143–157 (2007) (full paper available here), and really only definitively points to deforestation and Amaranth cultivation at that point in the highlands of Columbia.

From Wikipedia.

The population that replaced them, which is genetically linked to the speakers of Chibchan languages and probably originated in Central America, has remained the dominant population of the region in genetic continuity with their ancestors since this population replacement occurred, although later populations admixed with them and brought new languages in some parts of the region. 

There is no evidence that anyone from the pre-agricultural, pre-ceramic culture that was replaced in the Columbian highlands survived, or even significantly admixed with surviving populations.

The new agriculturalist culture did not really come into its own archaeologically until 1000 BCE to 800 BCE, so we can't know for sure if the replacement took place suddenly (although the lack of admixture between the new and old populations suggests that it did) or more gradually, or how long after maize cultivation, a thousand years earlier than this culture's pots appeared, the population replacement happened. 

Conservatively, it happened in some short time period between 1800 BCE and 800 BCE (about 3,000 to 4,000 years after it happened in Europe). Realistically, it probably happened on the later side of that time range when other components of the emerging farmer culture, like pottery and possibly other key domesticated plants and/or animals, joined with improved maize cultivation to give rise to a technologically dominant new culture.

The introduction and discussion sections of a new study released May 28, 2025 in the journal Scientific Advances by Kim-Louise Krettek, et al., explain that:

Genetic studies on ancient and present-day Indigenous populations have substantially contributed to the understanding of the settlement of the Americas. Those studies revealed that the population ancestral to non-Arctic Native Americans derives from a genetic admixture between ancient East Asian and Siberian groups somewhere in North-East Asia before 20,000 years before the present (yr B.P.). Around 16,000 yr B.P., after its arrival in North America, this genetic ancestry split into two lineages known as northern Native American and southern Native American. While northern Native American ancestry is largely confined to ancient and current populations of North America, the southern Native American lineage expanded further south and constitutes the main ancestry component of ancient and present-day Indigenous South Americans. 

Southern Native American ancestry diversified within North America into at least three sublineages, i.e., one related to the Clovis-associated Anzick-1 individual from western Montana (USA), one found in ancient California Channel Islands individuals and the last one representing the main ancestry source of modern-day Central and South Americans.  

Each of these sublineages provided a wave of ancestry into the gene pool of ancient South Americans. Individuals from Chile and Brazil dating back to around 12,000 and 10,000 yr B.P., respectively, were more genetically related to the Anzick-1 genome than individuals from the eastern Southern American coast, Southern Cone and the Andes from 10,000 yr B.P. onward. In addition, the California Channel Islands ancestry was found in the Central Andes by 4200 yr B.P. and became widespread in the region thereafter. However, the exact timing of these population movements into the southern subcontinent remains largely unsolved to date. 

The Isthmo-Colombian area, stretching from the coast of Honduras to the northern Colombian Andes, is critical to understanding the peopling of the Americas. Besides being the land bridge between North and South America, it is at the center of the three major cultural regions of Mesoamerica, Amazonia, and the Andes. At the time of European contact, the region was inhabited by a complex mosaic of human populations, mainly speakers of Chibchan, Chocoan, Carib, and Arawakan languages. 

Among those populations, those who were speakers of Chibchan languages were the most widespread in the region in terms of demography, cultural diversity, and territorial distribution. Chibchan is a language family with multiple, highly distinct branches, many of which are still spoken today in different regions of the Isthmo-Colombian area. The homeland and antiquity of the Proto-Chibchan language and the ancestor of all Chibchan languages remain subjects of debate. High intrafamily variation in terms of lexicon and grammar suggests that the language family is ancient and began diversifying several thousand years ago. The locus of that incipient diversification, however, is still uncertain. Most scholars believe that this protolanguage began to diversify in Lower Central America, where the largest number of these languages is spoken today. However, some evidence suggests that Proto-Chibchan might have originated in South America and then diversified in Central America at a much later date. 

Genetic studies of ancient and present-day Isthmo-Colombian Indigenous populations revealed a distinctive ancestry component primarily associated with speakers of Chibchan languages. However, whereas mitochondrial DNA (mtDNA) studies suggested a migration of Chibchan-related ancestry from Central America into Colombia and Venezuela, genome-wide studies favored an opposite, south-to-north population movement. According to the latter model, speakers of Chibchan languages from Central America are not direct descendants of the first settlers in the region but, instead, derive from a more recent back migration from South to Central America. 

The southernmost region of the Isthmo-Colombian area is the Altiplano Cundiboyacense (hereafter Altiplano). This plateau with an average altitude of 2600 m in the Eastern Cordillera of the Colombian Andes was inhabited by ancient hunter-gatherer groups from the Late Pleistocene. During the Early and Middle Holocene phases of the Preceramic period (~11,500 to 4000 yr B.P.), populations on the Altiplano underwent multiple cultural transformations, most notably increased sedentism and a transition from a hunter-gatherer subsistence to the introduction of horticultural practices and forest management. However, it was not until the early Late Holocene, ~3800 yr B.P., that the first clear evidence of maize cultivation appeared. 

During the subsequent Formative period (~3000 to 1000 yr B.P.), a distinct type of pottery emerged on the Altiplano that is referred to as the Herrera ceramic complex, also known in the literature as the Herrera period (2800 to 1200 yr B.P.). It is still highly debated whether Herrera-associated groups on the Altiplano derived from an in situ development of local hunter-gatherers or were a consequence of population dispersals into the region. 

Around 1200 yr B.P., a cultural phase, known as the Muisca period, began on the Altiplano and lasted until the imposition of the Hispanic Colonial regime in the mid-16th century. Most available evidence is suggestive of population continuity with the preceding Herrera period. The Muisca period is characterized by a relatively continuous process of demographic growth, development of agriculture and trade, and social and political complexification. These factors played a considerable role in shaping the Muisca culture and gave rise to the Chibchan-speaking population that dominated the Altiplano until European colonization. 

While several studies have reported mtDNA data from ancient Colombian individuals, genome-wide data from this region are still entirely lacking to date. In this study, we generated mtDNA and genome-wide data of 21 ancient individuals from two areas of the Altiplano (Bogotá plateau and Los Curos). Our data, spanning a time transect between around 6000 and 500 yr B.P., provide an opportunity to explore several key questions: 

(i) Which southern Native American genetic ancestry do Preceramic individuals from the Altiplano derive from? 

(ii) Were the cultural transformations associated with the Herrera and Muisca periods accompanied by migrations and demographic changes? 

(iii) How is the genetic ancestry observed in speakers of Chibchan languages related to that of ancient individuals from the Altiplano? 

(iv) What are the genetic relationships between the generated ancient genomes and the existing genomic data of present-day Indigenous communities from Colombia and neighboring regions?

In this study, we generated genome-wide data from 21 individuals spanning a time transect of almost 6000 years from the Altiplano, which represents the southern edge of the Isthmo-Colombian area. Our findings contribute to a better understanding of the population history of this area, a key region in the peopling process of South America. We show that the hunter-gatherer population from the Altiplano dated to around 6000 yr B.P. lack the genetic ancestry related to the Clovis-associated Anzick-1 genome and to ancient California Channel Island individuals, suggesting their affiliation to the southern Native American lineage that became the primary source of ancestry of South Americans by 9000 yr B.P. 

However, unlike ancient genomes from the Andes and the Southern Cone that are associated with the same wave of ancestry, the analyzed Preceramic individuals from Colombia do not share distinct affinity with any ancient or modern-day population from Central and South America studied to date. Colombia_Checua_6000BP can thus be modeled as a previously undescribed distinct lineage deriving from the radiation event that gave rise to multiple populations across South America during its initial settlement. 

The cultural transition between the Preceramic and Herrera periods is associated with a seemingly complete replacement of the local genetic profile. This challenges the model where local hunter-gatherers developed in situ as suggested by morphometric studies and an ancient mtDNA time transect. Instead, our study provides evidence for a major genetic turnover on the Altiplano occurring after 6000 yr B.P. but before 2000 yr B.P. Since the mechanisms and precise temporal scale of this replacement event remain uncertain, we cannot directly associate it with the emergence of maize cultivation ~3800 yr B.P. However, our data do support the archaeological hypothesis that the introduction of pottery associated with the Herrera ceramic complex was mediated through population dispersals. 

Our results show that the incoming genetic ancestry on the Altiplano is related to ancient and present-day populations speaking Chibchan languages from Central America. This can be explained most parsimoniously by Chibchan-related migrations from Lower Central America to South America, rather than back-migration to the isthmus. 

A separate study found evidence for a previously unknown south-to-north expansion of Chibchan-related ancestry from Lower Central America into the Mayan territories of Belize by 5600 yr B.P. Therefore, rather than modeling Central American populations associated with Chibchan languages as deriving from a mixture between North and South American ancestries, these results are consistent with an origin of Chibchan-related ancestries in Lower Central America, followed by bidirectional gene flow toward both Meso- and South America. This model of an original “Chibchan homeland” in Central America is supported not only by mtDNA studies on present-day populations who speak Chibchan languages but also from linguistic observations, indicating that the isthmus region exhibits the highest diversity within this language family. 

From an archaeological perspective, the Chibchan-related ancestry is first identified in 2000-year-old individuals associated with Herrera ceramics. In addition, previously sequenced Ceramic-associated individuals from Venezuela dated to 2400 yr B.P. also showed a high affinity to Central American populations speaking Chibchan languages. Despite the similar ancestry pattern and temporal frame, the two populations do not appear to form a simple sister group. This could be in line with linguistic evidence that suggests multiple, distinct Chibchan language expansions into South America, but additional studies will be necessary to further clarify this issue. 

After the arrival of the Chibchan-related ancestry, which completely reshaped the genetic landscape of the region, we find evidence of a long period of genetic continuity in the genetic profile of the local populations for over 1500 years (from at least 2000 to 500 yr B.P.). The stability in genetic ancestry encompasses the end of the Herrera period and the beginning of the Muisca period. This points to a scenario in which populations speaking languages from the Chibchan lineage would have settled the Altiplano before the emergence of traits normally associated with the Muisca culture, and it shows that this cultural transition took place without a substantial migration from regions with a distinct genetic ancestry composition. In addition, such a genetic continuity extends through different cultural phases within the Muisca period and persists until the Spanish colonization. Colonial linguistic documentation established that Muisca people spoke a now extinct Chibchan language. Our findings not only confirm their genetic link with speakers of Chibchan languages from Central America but also suggest that ancestral Chibchan languages, possibly basal to the Magdalenic branch that gave rise to the documented Muisca language, might have already been spoken on the Altiplano during the pre-Muisca Herrera period. 

While the representation of Indigenous populations in our dataset is certainly not exhaustive, the observed spatial pattern in the genetic affinity of post-2000 yr B.P. ancient Colombians with present-day Indigenous populations raises questions regarding the uneven distribution of populations speaking Chibchan languages across the Isthmo-Colombian area at the time of the Hispanic colonization, also referred to as a Chibchan “archipelago”. 

One possible explanation is that this distribution resulted from separate dispersals from Central America to different locations of northern South America rather than a single expansion wave, as suggested by the internal branching pattern of the Chibchan language family. However, it is also possible that the initial spread was more widespread and got later fragmented by post-Chibchan migration and admixture events. The observation that Chibchan-affiliated populations from northern Colombia have a significantly reduced genetic affinity to post-2000–yr B.P. ancient Colombians than to Lower Central Americans supports the role of population admixture in shaping the genetic diversity of northern South America.

Also, while the earlier South American hunter-gatherer clade that went extinct probably dated to the founding wave of the modern humans in South America, they did not have notable Australasian or Melanesian ancestry, disfavoring the existence of a dramatically genetically distinct founding population of the Americas that preceded the main founding wave of modern humans and has Australasian or Melanesian genetic affinities that ancient.

Early Homo Erectus In Spain And Where It Fits In The Larger Narrative

Overview

Anthropologists have found partial Homo erectus remains in Spain from 1.1-1.4 million years ago, adding to 1.97 million year old Homo erectus remains in Grăunceanu, Romania, and 1.77-1.85 million year old Homo erectus remains in Dmanisi, Georgia. 

Homo erectus first appears in Africa. Outside of Africa, Homo erectus remains are most often found in Indonesia and China, dating from around 108,000 years ago in Southeast Asia, back to about 70,000 years after this species evolved in Africa. 

Homo erectus went extinct in most of the world around 1,000,000 years ago, but persisted longer in Southeast Asia and possibly in East Asia, and relict populations of Homo erectus probably admixed with Denisovans at some point when both species existed. A major population bottleneck described below, probably took place in Homo erectus starting around 930,000 years ago, but it didn't result in the complete extinction of the species. Homo erectus was probably extinct by the time that modern humans first ventured beyond South Asia (not long after the Toba eruption ca. 75,000 years ago). It is plausible that the Toba eruption, followed by first contact with modern humans, may have led to the final extinction of Homo erectus, to the final extinction of H. floresiensis and H. luzonensis, and also to the extinction of Denisovans over most of their range (with the last relict Denisovans in Tibet probably going extinct in connection with their contacts with modern humans in this remote place).

We know that Homo erectus evolved in Africa rather than Eurasia, because that is where the species that Homo erectus evolved from, mostly likely H. habilis, but possibly some other African archaic hominin, was located at the time, and not just because the oldest Homo erectus remains are found there.

The oldest identified H. erectus specimen is a 2.04 million year old skull, DNH 143, from Drimolen, South Africa, coexisting with the australopithecine Paranthropus robustus. H. erectus dispersed out of Africa soon after evolution, the earliest recorded instances being H. e. georgicus 1.85 to 1.78 million years ago in Georgia and the Indonesian Mojokerto and Sangiran sites 1.8 to 1.6 million years ago.

(The quoted Wikipedia summary hasn't been updated to reflect the Romanian discovery announced earlier this year.)

Half a million years and a few hundred meters away from this site, there are Homo antecessor remains, from a time when Homo erectus had gone extinct in Europe, almost 700,000 years before Homo erectus went extinct in Asia.

The New Discovery

ATE7-1 fossil face (right) with mirrored 3D model (left). Credit: Maria D. Guillén / IPHES-CERCA / Elena Santos / CENIEH

When the global timeline passed one million years ago, more than half the span of hominin presence in Eurasia had already passed by. The earliest archaeological evidence in Eurasia is more than two million years old—found in places like Shangchen, China, and the Dawqara Formation of Jordan. Just this year Grăunceanu, Romania, joined the list of early archaeological traces of hominins in Europe, dating to an estimated 1.97 million years ago.

Still, I think about the threshold of one million years ago quite often. The number of sites in Eurasia with hominin evidence before one million years ago has grown quite large. It would have been hard to imagine this in 1990, when many scientists wondered if any sites in Eurasia were really older than this. Today there are many. And yet, the number of sites with fossils of hominins is quite a lot smaller than the number with stone artifacts or cutmarked animal bones. Most are in China or Indonesia, in addition to the exceptional site of Dmanisi, Georgia.

In western Europe there may be only two such sites, both in Spain: Sima del Elefante and Barranco Léon.

This week Rosa Huguet and collaborators have reported on a significant new addition to this very humble record. In work at Sima del Elefante in 2022, excavators uncovered a fragmentary facial skeleton, designated as ATE7-1. The estimated age of this fossil face is between 1.4 million and 1.1 million years ago. The new fossil joins two other hominin fossils from this cave deposit, within the same range of ages, a finger bone and a fragment of the front portion of a mandible with several worn teeth, ATE9-1. These fossils have been previously published, the mandible in 2008.

None of these fossils provide much to go on. Huguet and coworkers compared the facial anatomy of ATE7-1 with fossil faces attributed to Homo erectus from Dmanisi, Georgia, and Sangiran, Indonesia. They also compared the face to fossils from Gran Dolina, Spain, attributed to Homo antecessor. This site is located only a few hundred meters from Sima del Elefante but represents hominins and stone artifacts from around 780,000 years ago—as much as a half million years or more later than Sima del Elefante.

The ATE7-1 face is more like most H. erectus faces than either is like the later Gran Dolina fossils.

From John Hawks.

Context

Where does this discovery fit in the larger narrative of archaic hominin evolution?

Neanderthals, Denisovans, and modern humans (i.e. Homo sapiens) all share a Homo erectus ancestor and probably also at least one intermediate archaic hominin ancestor that evolved from Homo erectus.

The oldest archaeological evidence of modern humans, which is, order of magnitude consistent with age estimates for the most recent common ancestor of all modern human uniparental Y-DNA and mtDNA lineages, is about 300,000 years ago in Africa. Modern humans first left Africa around 125,000 to 100,000 years ago, and did so via the Middle East rather than Iberia. But the lion's share of non-African modern humans appear to be descended from a later wave of modern human expansion out of Africa about 50,000-74,000 years ago, with the lion's share of that wave closer to 50,000 years ago than 74,000 years ago. Neanderthal populations largely stalled this expansion into Europe until about 40,000 years ago. One or more of the hominin populations of Southeast Asia, and the jungles of Southeast Asia, probably stalled modern human expansion via the Southern route into Asia until around the time of the Toba eruption around 74,000 years ago (with the eruption possibly weakening these barriers and possibly also creating a reason for the modern humans of South Asia to expand to the Southeast).

The oldest Neanderthal remains are about 430,000 years old. Neanderthals were moribund by 40,000 years ago (with modern human Cro-Magnon people entering Europe around the same time that Neanderthals became extinct and overlapping with them for periods of a thousand or two thousand years or so in any one place), with the final relict population going extinct around 29,000 years ago. The leading explanations for Neanderthal extinction include a wave of volcanic eruptions, climate change, and the growing superiority of modern human hunter-gatherers due to their cultural evolution (e.g. stone technologies and the domestication of dogs) and/or genetic evolution. The range of Neanderthals extended from Northern Wales to the Middle East to South Asia and the Altai Mountains. There was significant Neanderthal admixture with modern humans, probably around 50,000-100,000 years ago (the latest estimates tend to favor a more recent date) in the vicinity of the Middle East or Iran (leaving a DNA legacy in all non-African modern humans), and there was also a more modern admixture with Altai Neanderthals (leaving a DNA legacy in Asian modern humans). Non-Africans today have up to 2% Neanderthal DNA, with Asians having a little more than Europeans, although ancient DNA from modern humans in ancient Eurasia, much closer to Neanderthal admixture sometimes have higher percentages of Neanderthal admixture. Neanderthals had bigger brains than modern humans, but also a more static material culture and less diverse range of hunting prey heavily concentrated around large megafauna (suggesting reduced brain plasticity and less ability to adapt culturally rather than genetically), with modern humans also relied on a wider array of smaller prey like rabbits, smaller birds, fish, and other seafood. At the time of first contact with modern humans, the effective population size of Neanderthals was about ten times smaller than the effective population size of modern human Cro-Magnons, and the effective Neanderthal effective population size ranged from about 3,000-12,000 throughout their existence and was fractured into multiple more or less isolated regional subpopulations.

Wikipedia says this about the extinction of Neanderthals:

The extinction of Neanderthals was part of the broader Late Pleistocene megafaunal extinction event. Neanderthals were replaced by modern humans, indicated by the near-complete replacement of Middle Palaeolithic Mousterian stone technology with modern human Upper Palaeolithic Aurignacian stone technology across Europe (the Middle-to-Upper Palaeolithic Transition) from 41,000 to 39,000 years ago. Iberian Neanderthals possibly persisted until about 35,000 years ago, modern human expansion perhaps impeded by the Ebro River. Neanderthals in Gibraltar may have survived as late as 28,000 years ago at Gorham's Cave. The dating of these late Iberian sites is contested.

Historically, the cause of extinction of Neanderthals and other archaic humans was viewed under an imperialistic guise, with the superior invading modern humans exterminating and replacing the inferior species.

When sapiens began to expand and spread, he eliminated the other contemporary races [including Neanderthals] just as the white man drove out the Australian aborigines and the North American Indians.

— Ernst Mayr, 1950

The assimilation of Neanderthal populations into modern human populations had long been hypothesised with supposed hybrid specimens, and was revitalised with the discovery of archaic human DNA in modern humans. Similarly, the Châtelperronian industry of central France and northern Spain may represent a culture of Neanderthals adopting modern human techniques, via acculturation. Other ambiguous transitional cultures include the Italian Uluzzian industry, and the Balkan Szeletian industry.

Aside from competition with modern humans, Neanderthal extinction has also been ascribed to their low population as well as the resulting mutational meltdown, making them less adaptable to major environmental changes (specifically Heinrich event 4) or new diseases.

The admixture between modern humans and Neanderthals went in both directions. And, some of the late archaeological tool cultures of Neanderthal, which coincide with the arrive of modern humans in Europe, may reflect the increased brain plasticity of hybrid Neanderthal-modern human individuals.

Denisovans (named after the cave in the Altai where the type remains were discovered) probably existed from at least 285,000 years ago to about 25,000 years ago, general in Asia to the east of the Neanderthal range from Altai and Tibet to Southeast Asia, and overlapping with the Neanderthal range in the Altai region. High altitude adaptation DNA admixed from Denisovans are found in Tibetans. Trace levels of Denisovan admixture are found in mainland Southeast Asia and East Asia, and in island Southeast Asia up to the Wallace Line. Modern humans with Australian aboriginal ancestry or Papuan ancestry or Filipino negrito ancestry have substantial Denisovan ancestry (up to 6%) in addition to their Neanderthal ancestry (up to 2%). Presumably, the Denisovan-modern human admixture whose legacies exist in Australian aborigines, Papuans, Filipino negritos, and mainland Southeast Asians and East Asians must have occurred around the time of first contact between the first wave of modern humans in Asia around 50,000 to 75,000 years ago, and was then greatly diluted by subsequent waves of modern human migration west of the Wallace line in Asia. Also, Denisovans presumably went extinct within a thousand or two thousand years or so of first contact with modern humans (which took place much later in Tibet than almost everywhere else).

The exact path from Homo erectus to modern humans, Neanderthals, and Denisovans (and possibly other now extinct archaic species derived from Homo erectus) is a matter of ongoing investigation and debate.

Denisovan mtDNA diverged from that of modern humans and Neanderthals about 1,313,500–779,300 years ago; whereas modern human and Neanderthal mtDNA diverged 618,000–321,200 years ago. Krause and colleagues then concluded that Denisovans were the descendants of an earlier migration of H. erectus out of Africa, completely distinct from modern humans and Neanderthals.

However, according to the nuclear DNA (nDNA) of Denisova 3—which had an unusual degree of DNA preservation with only low-level contamination—Denisovans and Neanderthals were more closely related to each other than they were to modern humans. Using the percent distance from human–chimpanzee last common ancestor, Denisovans/Neanderthals split from modern humans about 804,000 years ago, and from each other 640,000 years ago. 

Using a mutation rate of 1×10^−9 or 0.5×10^−9 per base pair (bp) per year, the Neanderthal/Denisovan split occurred around either 236–190,000 or 473–381,000 years ago respectively. Using 1.1×10^−8 per generation with a new generation every 29 years, the time is 744,000 years ago. Using 5×10^−10 nucleotide site per year, it is 616,000 years ago. Using the latter dates, the split had likely already occurred by the time hominins spread out across Europe. 

H. heidelbergensis is typically considered to have been the direct ancestor of Denisovans and Neanderthals, and sometimes also modern humans. Due to the strong divergence in dental anatomy, they [i.e. Denisovans] may have split before characteristic Neanderthal dentition evolved about 300,000 years ago.

The more divergent Denisovan mtDNA has been interpreted as evidence of admixture between Denisovans and an unknown archaic human population, possibly a relict H. erectus or H. erectus-like population about 53,000 years ago. Alternatively, divergent mtDNA could have also resulted from the persistence of an ancient mtDNA lineage which only went extinct in modern humans and Neanderthals through genetic drift. Modern humans contributed mtDNA to the Neanderthal lineage, but not to the Denisovan mitochondrial genomes yet sequenced. The mtDNA sequence from the femur of a 400,000-year-old H. heidelbergensis from the Sima de los Huesos Cave in Spain was found to be related to those of Neanderthals and Denisovans, but closer to Denisovans, and the authors posited that this mtDNA represents an archaic sequence which was subsequently lost in Neanderthals due to replacement by a modern-human-related sequence.

The intermediate species that is the most recent common ancestor of Neanderthals, Denisovans, and modern humans probably arose not long after a genetic bottleneck which has been inferred from modern DNA. This genetic bottleneck probably occurred in the clade of H. erectus which is ancestral to modern humans. As one secondary source explaining this notes:

Between 930,000 and 813,000 years ago, something nearly ended humanity before it even began. A mysterious bottleneck reduced the human breeding population to just 1,280 individuals, pushing our ancestors to the brink of extinction for an astonishing 117,000 years. 

Scientists have long puzzled over a gap in the African and Eurasian fossil records, and now, a team of researchers may have found the answer. Using a groundbreaking method called FitCoal, they analyzed the genomes of 3,154 modern humans to reconstruct ancient population sizes. What they found was staggering. Nearly 99% of early humans vanished, likely due to extreme climate events such as glaciations, severe droughts, and the collapse of ecosystems.

The world was changing. Glaciation, extreme droughts, and collapsing ecosystems made survival nearly impossible. Food sources vanished, and so did most of our ancestors. Those who remained – just a tiny fraction of the original population – fought to endure in a harsh and unpredictable environment. 

But against all odds, they survived. And in doing so, they may have changed the course of human evolution forever. Scientists believe this bottleneck could have led to the merging of two ancestral chromosomes, forming what we now know as chromosome 2 – a key feature that separates modern humans from other primates.

Around 813,000 years ago, the climate began to shift. Our ancestors may have mastered fire, allowing them to cook food, stay warm, and fend off predators. Populations rebounded, and from that tiny group of survivors, the future of humanity was born. 

This discovery reshapes our understanding of human history, and raises new questions. Where did these survivors live? How did they overcome such extreme conditions? Did this struggle push human intelligence to evolve faster?

The paper that is the basis for this account is Wangjie Hu, et al., "Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition" 381(6661) Science 979-984 (August 31, 2023). Its abstract materials state:

Editor’s summary 

Today, there are more than 8 billion human beings on the planet. We dominate Earth’s landscapes, and our activities are driving large numbers of other species to extinction. Had a researcher looked at the world sometime between 800,000 and 900,000 years ago, however, the picture would have been quite different. Hu et al. used a newly developed coalescent model to predict past human population sizes from more than 3000 present-day human genomes (see the Perspective by Ashton and Stringer). The model detected a reduction in the population size of our ancestors from about 100,000 to about 1000 individuals, which persisted for about 100,000 years. The decline appears to have coincided with both major climate change and subsequent speciation events. —Sacha Vignieri 

Abstract 

Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.

The proposed climate event was part of the Mid-Pleistocene Transition. Some key aspects of this, in places where Homo erectus reached, were as follows:

Europe

In Europe, the MPT was associated with the Epivillafranchian-Galerian transition and may have led to the local extinction of, among other taxa, Puma pardoides, Megantereon whitei, and Xenocyon lycaonoides. The prevalence of ungulates adapted for grazing increased in the Mediterranean region after the "0.9 Ma event". The northern North Sea Basin was first glaciated during the MPT. The increased intensity of transgressive-regressive cycles is recorded in northern Italy.

Asia

The cooling brought about by the MPT increased westerly aridity in the western Tarim Basin. East Asian Summer Monsoon (EASM) precipitation declined. Grasslands expanded across the North China Plain as forests contracted.

During the MPT, the Indian Summer Monsoon (ISM) decreased in strength. In the middle of the MPT, there was a sudden decrease in denitrification, likely due to increased solubility of oxygen during lengthened glacial periods. After the MPT, the Bay of Bengal experienced increased stratification as a result of the strengthening of the ISM, which resulted in increased riverine flux, inhibiting mixing and creating a shallow thermocline, with stratification being stronger during interstadials than stadials. Paradoxically, variability in Δδ18O in the Bay of Bengal between glacials and interglacials decreased following the MPT.

Africa

In Central Africa, detectable floral changes corresponding to glacial cycles were absent prior to the MPT. Following the MPT, a clear cyclicity became evident, with interglacials being characterised by warm and dry conditions while glacials were cool and humid.

According to one of the leading papers on the 0.9 Ma Event, closely associated with the Homo erectus genetic bottleneck:

The Early-Middle Pleistocene Transition (EMPT) (ca. 1.4–0.4 Ma) represents a fundamental transformation in the Earth's climate state, starting at 1.4 Ma with a progressive increase in the amplitude of climatic oscillations and the establishment of strong asymmetry in global ice volume cycles. The progressive shift from a 41kyr–100kyr orbital rhythm was followed by the first major build-up of global ice volume during MIS 24-22, the so-called “0.9 Ma event”. The Vallparadís Section (Vallès-Penedès Basin, NE Iberian Peninsula) is one of the few Pleistocene series in Europe that spans the onset of the transition (from 1.2 to 0.6 Ma), thus representing a pivotal array of localities to investigate the effect of glacial dynamics on environmental conditions in Southern Europe. Here we inspect the effects of the EMPT on terrestrial ecosystems by examining the dietary adaptations (through dental meso- and microwear patterns) of fossil ungulates from the Vallparadís Section dated before and after the “0.9 Ma event”. Results show a steady presence of open grasslands before MIS 22 and more humid conditions at MIS 21. Both before and after MIS 22, a consistent presence of ungulates with long-term patterns that point to a grazing or grass-rich mixed feeding behaviour is observed, while noticeably, short-term patterns point to increased seasonality right after the “0.9 Ma event” glacial period. This increment of seasonality may have had an important effect on the Mediterranean habitats leading to recurring changes in the quality of plant resources available to large herbivores, which in response periodically adopted more mixed feeding behaviours widening their dietary breadth to consume also sub-optimal food items during adverse seasons.

In particular, during this event, global ice volumes increased substantially, and the Northern Hemisphere experienced increased seasonality and aridity, and surface sea temperatures in the North Atlantic reached their lowest values during the EMPT at this time. Also, grasslands expanded across the North China Plain as forests contracted.

This hypothesis is model dependent, could be impacted by sources of systemic error, like the possible much later extinction of Homo erectus populations derived from the same source population, later hard genetic sweeps of Homo erectus source genes, the effective extinction of modern humans arising from other clades of Homo erectus at some much later time, a lack of consideration of Neanderthal or Denisovan genes in the analysis, and a complete lack of ancient Homo erectus genomes. 

Also, in understanding this narrative one has to recognize that genetics researchers call an "effective population" of 1,280 individuals could have involved a census population at any one time that was many times larger than that. And, this is still about five times as large as the effective population size of the founding population of the Americas, for example. So, the bottleneck wasn't quite as extreme as some popular accounts of it would imply.

But the oldest examples of the species Homo antecessor does first appear in Europe, shortly after this inferred bottleneck, and there are no Homo erectus remains in Europe during or after the time of this inferred bottleneck.

Homo antecessor (Latin "pioneer man") is an extinct species of archaic human recorded in the Spanish Sierra de Atapuerca, a productive archaeological site, from 1.2 to 0.8 million years ago during the Early Pleistocene. Populations of this species may have been present elsewhere in Western Europe, and were among the first to settle that region of the world, hence the name. The first fossils were found in the Gran Dolina cave in 1994, and the species was formally described in 1997 as the last common ancestor of modern humans and Neanderthals, supplanting the more conventional H. heidelbergensis in this position. H. antecessor has since been reinterpreted as an offshoot from the modern human line, although probably one branching off just before the modern human/Neanderthal split.

Despite being so ancient, the face is unexpectedly similar to that of modern humans rather than other archaic humans—namely in its overall flatness as well as the curving of the cheekbone as it merges into the upper jaw—although these elements are known only from a juvenile specimen. Brain volume could have been 1,000 cc (61 cu in) or more, but no intact braincase has been discovered. This is within the range of variation for modern humans. Stature estimates range from 162.3–186.8 cm (5 ft 4 in – 6 ft 2 in). H. antecessor may have been broad-chested and rather heavy, much like Neanderthals, although the limbs were proportionally long, a trait more frequent in tropical populations. The kneecaps are thin and have poorly developed tendon attachments. The feet indicate H. antecessor walked differently than modern humans.

H. antecessor was predominantly manufacturing simple pebble and flake stone tools out of quartz and chert, although they used a variety of materials. This industry has some similarities with the more complex Acheulean, an industry which is characteristic of contemporary African and later European sites. Groups may have been dispatching hunting parties, which mainly targeted deer in their savannah and mixed woodland environment. Many of the H. antecessor specimens were cannibalised, perhaps as a cultural practice. There is no evidence they were using fire, and they similarly only inhabited inland Iberia during warm periods, presumably retreating to the coast otherwise.

Meanwhile:

Homo heidelbergensis (also H. erectus heidelbergensis, H. sapiens heidelbergensis) is an extinct species or subspecies of archaic human which existed from around 600,000 to 300,000 years ago, during the Middle Pleistocene. Homo heidelbergensis was widely considered the most recent common ancestor of modern humans and Neanderthals, but this view has been increasingly disputed since the late 2010s.

In the Middle Pleistocene, brain size and height were comparable to modern humans. Like Neanderthals, H. heidelbergensis had a wide chest and robust frame.

Fire likely became an integral part of daily life after 400,000 years ago, and this roughly coincides with more permanent and widespread occupation of Europe (above 45°N), and the appearance of hafting technology to create spears. H. heidelbergensis may have been able to carry out coordinated hunting strategies, and consequently they seem to have had a higher consumption of meat.

It is debated whether or not to constrain H. heidelbergensis to only Europe or to also include African and Asian specimens, and this is further confounded by the type specimen (Mauer 1) being a jawbone, because jawbones feature few diagnostic traits and are generally missing among Middle Pleistocene specimens.

H. heidelbergensis was subsumed in 1950 as a subspecies of H. erectus but today it is more widely classified as its own species. H. heidelbergensis is regarded as a chronospecies, evolving from an African form of H. erectus (sometimes called H. ergaster).

At least three other archaic hominin species overlapped with hominins from the H. erectus era or later.

• Homo floresiensis – Extinct small human species found in Flores
• Homo luzonensis – Archaic human from Luzon, Philippines
• Homo naledi – South African archaic human species

H. floresiensis and H. luzonensis may have been regional variations of the same species and show similarities with each other. The most plausible theory of their phylogenetic position, in my view, is that both of them were sub-species of H. habilis, and may have left Africa, either independently, or together with either H. erectus, the Denisovan ancestor, or Denisovans themselves. H. floresiensis and Denisovans (and possibly the earliest modern humans to arrive there as well) may have co-existed on the island of Flores, Indonesia (which is past the Wallace line) at some point in  time. There are no remains of H. floresiensis, H. luzonensis, H. habilis, or any other archaic hominins before H. erectus disperses from Africa. 

H. naledi was a South African archaic hominin species that flourished from 335,000 to 226,000 years ago, that was probably not directly ancestral to modern humans or any other non-African archaic hominins, but would have co-existed in time (and possibly space) with the earliest modern humans in Africa.

A November 6, 2024 post at this blog recapped some other possible non-African archaic hominins who existed at the same time that modern humans did: 

Notably the remains of the Red Deer Cave People of China from 14,000 years ago (a few thousand years before the start of the Holocene era) are genetically modern humans and are not archaic hominins despite some of their seemingly archaic features. See also here.

I am also inclined to think that they may yet be a small relict population of small archaic hominins in a remote Indonesian jungle on the island of Sumatra and perhaps Flores as well, where these cryptids, called Orang Pendek, locally, have been attested but not definitively confirmed to still exist. I discuss this further at this post.

Homo floresiensis (discovered in 2003) are commonly known as "hobbits" and have been found on the island of Flores. Their phylogeny is disputed, but I find the theory that they are an asian branch of H. habilis to be most convincing. H. luzonesis (discovered in 2007) is similar and contemporaneous, but found further east in the Philippines and is supported by a less complete archaeological record. Both of these diminutive species are found in association with late Pleistocene tools and "oriental fauna".

Personally, being more of a lumper than a splitter, I'm inclined to see H. floresiensis and H. luzonesis as sub-species variations of the same species ("race" within that species to use some outdated terminology), and likewise to see H. longi, H. juluensis, and Denisovans as sub-species variations of the Denisovan species. The Hualongdong archaic hominin fossils ... could be a hybrid individual, perhaps a Neanderthal-Denisovan hybrid individual (something that has precedent in a Denisovan cave DNA sample).

Academic anthropologists, in contrast, tend to be splitters, in part, because it is cool and career advancing to discover and name your own archaic species, in part because the data is so fragmentary that grouping different fragmentary remains in a clade presumes relationships between the remains that aren't solidly proven, and in part, because it is easy to underestimate how much morphological diversity is possible within a single species if populations of it exposed to different environmental conditions.

H. longi a.ka. "dragon man" dates to an earlier time period (still contemporaneous with modern humans in Africa) in China and Manchuria, was discovered in 1933, and has been hypothesized to be a sister clade to Neanderthals, Denisovans, and modern humans, and a descendant of the pre-modern human hominin species H. antecessor due in part to basal archaic features in the skull.

H. juluensis (literally "big heads") is contemporaneous H. longi, and beyond that time frame into the time frame of H. floresiensis and was discovered from 1976-1979 in China and Tibet. The authors assign this specimen along with Xiahe and Penghu fossils, to the Denisovan species (a sister clade to Neanderthals and modern humans) based upon comparisons of their fossil teeth and rough geographic proximity. H. juluensis is found in association with early Paleolithic tools and remains of Paleoarctic fauna. But they have larger brain cases than H. longi. A previous suggestions of the link between H. longi and the Denisovan species are discussed here and here at this blog. At least one Denisovan tooth has been found in Laos dated to 131,000 years ago.

The article also discusses the Hualongdong archaic hominin fossils that "date to the late Middle Pleistocene (~300,000 years BP) and display a mosaic of characteristics that cannot be easily fitted into any one lineage," although they are closer to H. longi and H. juluensis. This individual could be a hybrid between these two subspecies, with H. erectus, or with a Neanderthal who was far east of his usual range.

Prior to 2021, H. longi and H. juluensis tended to be classified as H. erectus (remains of which start to appear at a much greater time depth in Asia) or as archaic modern humans.

The Narmada and Maba partial skulls, especially the latter, are suggestively associated with Neanderthals by the article.

These Asian archaic species also overlap in time with the Southern African archaic hominin clade H. naledi which is a sister clade to the modern human ancestors and to the common ancestor of modern humans, Neanderthals, and Denisovans, but is not actually among our ancestors. As I explained at the link, this species "is basically a story from The Silmarillion of hominin evolution. It is entertaining, especially for hard core human evolution fans, but it doesn't really advance the plot."

A small number of papers reported genetic evidence in modern Africans of admixture with an archaic hominin "ghost species" in Africa, but subsequent papers have explained this "ghost species" signal as a methodological artifact that merely arises from population structure in early modern human Africans (see also here). But there may have been relict archaic hominins that did not admix with modern humans in Africa that were also contemporaneous with modern humans, at least, early on.

The question of whether behaviorally modern humans started showing advanced behavior around 70,000-50,000 years ago (at the dawn of the Upper Paleolithic era and close in time to the Out of Africa event for modern humans), was associated with an evolutionary leap in their brains is an open and unresolved question. See also here (addressing the question of what made modern humans genetically distinct from archaic hominins).

Austronesian-Papuan People Replaced The First Modern Humans In Wallacea

Wallacea is the ecological region between the Wallace Line and the Lydekker Line (image via Wikipedia at the link). The plants and animals there differ greatly from those to the west (which were connected by land to mainland Asia when sea levels were lower) because neither animals nor 46,000 years of settlers after the first modern humans to cross into it, could cross the roughly 30 miles of deep sea between the regions.

The most basal modern human populations outside Africa, which also have the greatest Denisovan admixture, are the indigenous people of Papua New Guinea and Australia. People from this wave were also present on the islands of the Wallacean Archipelago in Indonesia and lived there undisturbed for about 46,000 years. 

But, when Papuans made contact with and fused with Austronesian sea farers (who originated on the island that is now called Taiwan) around 3500 years ago, contemporaneously with the late Bronze Age in Europe, the resulting fused population replaced the descendants of the first wave of modern humans in the Wallacean Achipelago.

Significance

We present a comprehensive study of the human genetic history of the Wallacean Archipelago and West Papuan regions of Indonesia, including 254 newly sequenced genomes, mostly from previously undocumented populations. In combination with linguistic and archaeological evidence, we show that Wallacean societies were transformed by the spread of genes and languages from West Papua in the past 3,500 y—the same period that Austronesian seafarers were actively mixing with Wallacean and Papuan groups. These migrant groups have largely replaced local Wallacean ancestry sources, challenging common assumptions that Papuan-related ancestry in Wallacea descends from first human migrants enroute to Sahul >50,000 y ago, and suggesting that these ancient movements may not be readily recoverable from modern genetic data alone.

Abstract

The tropical archipelago of Wallacea was first settled by anatomically modern humans (AMH) by 50 thousand years ago (kya), with descendent populations thought to have remained genetically isolated prior to the arrival of Austronesian seafarers around 3.5 kya. 

Modern Wallaceans exhibit a longitudinal countergradient of Papuan- and Asian-related ancestries widely considered as evidence for mixing between local populations and Austronesian seafarers, though converging multidisciplinary evidence suggests that the Papuan-related component instead comes primarily from back-migrations from New Guinea. 

Here, we reconstruct Wallacean population genetic history using more than 250 newly reported genomes from 12 Wallacean and three West Papuan populations and confirm that the vast majority of Papuan-related ancestry in Wallacea (~75 to 100%) comes from prehistoric migrations originating in New Guinea and only a minor fraction is attributable to the founding AMH settlers. 

Mixing between Papuan and local Wallacean lineages appears to have been confined to the western and central parts of the archipelago and likely occurred contemporaneously with the widespread introduction of genes from Austronesian seafarers—which now comprise between ~40 and 85% of modern Wallacean ancestry—though dating historical admixture events remains challenging due to mixing continuing into the Historical Period. In conjunction with archaeological and linguistic records, our findings point to a dynamic Wallacean population history that was profoundly reshaped by the spread of Papuan genes, languages, and culture in the past 3,500 y.

Gludhug A. Purnomo , Shimona Kealy, Sue O’Connor, Raymond Tobler, et al., "The genetic origins and impacts of historical Papuan migrations into Wallacea" 121 (52) PNAS e2412355121 (December 17, 2024). Hat tip to DDeden.

East Asian Historical Population Genetics Reviewed

A December 3, 2024 (open access) monograph published by the Cambridge University Press comprehensively reviews the historical population genetics of East Asia and its vicinity, with associated linguistic and cultural implications. It is one volume in a larger series about Ancient East Asia.

I'll discuss and analyze this wide ranging 90 page review article as time allows in the future. 

Hat tip to Language Log.

Archaic Hominins That Were Contemporaneous With Modern Humans

There were at least eight named non-H. sapiens archaic hominin species that existed in time periods overlapping those of  modern humans, H. sapiens, who evolved around 300,000 years ago. All were in the "Old World". There is no credible evidence that archaic hominin ever made it to the Americas, Australia, New Zealand, or most of the other islands of Oceania beyond island southeast Asia.

One was H. erectus that went extinct around 100,000 years ago after more than two million years roaming the Old World, first in Africa and later in Asia. There were also two hobbit-like species in island Southeast Asia, three East Eurasian sister clades to modern humans, the small but not hobbit-like H. naledi in Southern Africa, and Neanderthals in West Eurasia, although some of these species may actually be regional variants of the same species. 

All of these archaic hominin species had gone extinct (with the possible extended duration of a small isolated relict population or two, perhaps H. floresiensis) by about 29,000 years ago, leaving modern humans as the sole survivors (although some modern humans have Neanderthal ancestry (up to about 2%) from admixture events starting around 100,000 years ago, and some modern humans have both Neanderthal and also up to about 6% Denisovan ancestry, although absolute percentages are harder to estimate than percentages relative to other individuals with the same kind of introgression) from admixture events around the time that modern humans reached Southeast Asia. Incidentally, the introgression went both ways, with Neanderthals having up to 6% modern human introgressed ancestry, possibly due to events as much as 250,000 years ago. These sister clades capable of producing hybrid offspring may have been regionally specialized into climate niches.

Notably the remains of the Red Deer Cave People of China from 14,000 years ago (a few thousand years before the start of the Holocene era) are genetically modern humans and are not archaic hominins despite some of their seemingly archaic features. See also here.

I am also inclined to think that they may yet be a small relict population of small archaic hominins in a remote Indonesian jungle on the island of Sumatra and perhaps Flores as well, where these cryptids, called Orang Pendek, locally, have been attested but not definitively confirmed to still exist. I discuss this further at this post.

Homo floresiensis (discovered in 2003) are commonly known as "hobbits" and have been found on the island of Flores. Their phylogeny is disputed, but I find the theory that they are an asian branch of H. habilis to be most convincing. H. luzonesis (discovered in 2007) is similar and contemporaneous, but found further east in the Philippines and is supported by a less complete archaeological record. Both of these diminutive species are found in association with late Pleistocene tools and "oriental fauna".

Personally, being more of a lumper than a splitter, I'm inclined to see H. floresiensis and H. luzonesis as sub-species variations of the same species ("race" within that species to use some outdated terminology), and likewise to see H. longi, H. juluensis, and Denisovans as sub-species variations of the Denisovan species. The Hualongdong archaic hominin fossils, might be another hybrid individual or could be a hybrid individual, perhaps a Neanderthal-Denisovan hybrid individual (something that has precedent in a Denisovan cave DNA sample). 

Academic anthropologists, in contrast, tend to be splitters, in part, because it is cool and career advancing to discover and name your own archaic species, in part because the data is so fragmentary that grouping different fragmentary remains in a clade presumes relationships between the remains that aren't solidly proven, and in part, because it is easy to underestimate how much morphological diversity is possible within a single species if populations of it exposed to different environmental conditions.

H. longi a.ka. "dragon man" dates to an earlier time period (still contemporaneous with modern humans in Africa) in China and Manchuria, was discovered in 1933, and has been hypothesized to be a sister clade to Neanderthals, Denisovans, and modern humans, and a descendant of the pre-modern human hominin species H. antecessor due in part to basal archaic features in the skull. 

H. juluensis (literally "big heads") is contemporaneous H. longi, and beyond that time frame into the time frame of H. floresiensis and was discovered from 1976-1979 in China and Tibet. The authors assign this specimen along with Xiahe and Penghu fossils, to the Denisovan species (a sister clade to Neanderthals and modern humans) based upon comparisons of their fossil teeth and rough geographic proximity. H. juluensis is found in association with early Paleolithic tools and remains of Paleoarctic fauna. But they have larger brain cases than H. longi. A previous suggestions of the link between H. longi and the Denisovan species are discussed here and here at this blog. At least one Denisovan tooth has been found in Laos dated to 131,000 years ago.

The article also discusses the Hualongdong archaic hominin fossils that "date to the late Middle Pleistocene (~300,000 years BP) and display a mosaic of characteristics that cannot be easily fitted into any one lineage," although they are closer to H. longi and H. juluensis. This individual could be a hybrid between these two subspecies, with H. erectus, or with a Neanderthal who was far east of his usual range.

Prior to 2021, H. longi and H. juluensis tended to be classified as H. erectus (remains of which start to appear at a much greater time depth in Asia) or as archaic modern humans.

The Narmada and Maba partial skulls, especially the latter, are suggestively associated with Neanderthals by the article.

These Asian archaic species also overlap in time with the Southern African archaic hominin clade H. naledi which is a sister clade to the modern human ancestors and to the common ancestor of modern humans, Neanderthals, and Denisovans, but is not actually among our ancestors. As I explained at the link, this species "is basically a story from The Silmarillion of hominin evolution. It is entertaining, especially for hard core human evolution fans, but it doesn't really advance the plot."

A small number of papers reported genetic evidence in modern Africans of admixture with an archaic hominin "ghost species" in Africa, but subsequent papers have explained this "ghost species" signal as a methodological artifact that merely arises from population structure in early modern human Africans (see also here). But there may have been relict archaic hominins that did not admix with modern humans in Africa that were also contemporaneous with modern humans, at least, early on.

The question of whether behaviorally modern humans started showing advanced behavior around 70,000-50,000 years ago (at the dawn of the Upper Paleolithic era and close in time to the Out of Africa event for modern humans), was associated with an evolutionary leap in their brains is an open and unresolved question. See also here (addressing the question of what made modern humans genetically distinct from archaic hominins).

A greater degree of Late Quaternary hominin morphological variability is present in eastern Asia than previously assumed. Indeed, a number of distinct populations are present, some that now have new specific names: Homo floresiensis; H. luzonensis; H. longi; H. juluensis. With this piece, we describe the various groupings based on the current hominin fossil record of eastern Asia.

Christopher J. Bae & Xiujie Wu, "Making sense of eastern Asian Late Quaternary hominin variability" 15 Nature Communications 9479 (November 2, 2024) (opoen access) (hat tip to neo).