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.

The History And Prehistory Of Human Disease

A new paper in Nature concludes from ancient DNA that while infectious diseases were common in humans since the hunter-gatherer era, that there was a real surge, not at the time of the Neolithic Revolution, but when steppe herders started to invade and conquerer farmers, and hunter-gatherers, possibly because they lived more closely with their animals and because the diseases that they carried helped facilitate their conquests. The New York Times also discusses the paper.

Infectious diseases have had devastating effects on human populations throughout history, but important questions about their origins and past dynamics remain. To create an archaeogenetic-based spatiotemporal map of human pathogens, we screened shotgun-sequencing data from 1,313 ancient humans covering 37,000 years of Eurasian history. We demonstrate the widespread presence of ancient bacterial, viral and parasite DNA, identifying 5,486 individual hits against 492 species from 136 genera. Among those hits, 3,384 involve known human pathogens, many of which had not previously been identified in ancient human remains. Grouping the ancient microbial species according to their likely reservoir and type of transmission, we find that most groups are identified throughout the entire sampling period. Zoonotic pathogens are only detected from around 6,500 years ago, peaking roughly 5,000 years ago, coinciding with the widespread domestication of livestock. Our findings provide direct evidence that this lifestyle change resulted in an increased infectious disease burden. They also indicate that the spread of these pathogens increased substantially during subsequent millennia, coinciding with the pastoralist migrations from the Eurasian Steppe

Martin Sikora, et al., "The spatiotemporal distribution of human pathogens in ancient Eurasia" Nature (July 9, 2025).

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.

Homo Longi Were Denisovans

The archaic hominin skull from China provisionally classified as a member of the species Homo Longi has been linked to Denisovan DNA and proteins. This also makes it possible to know what a Denisovan looked like as shown in the image below.

The connection has been suspected, but not proven, for some time.

Human Migration To South America

A new, rather mediocre, study that emphasizes genetic diversity in South America tends to track the New World settlement paradigm rather closely. Honestly, for a major new paper in a major scientific journal, it adds surprisingly little to existing knowledge. 

Uncontacted or recently contacted populations in Amazonia and Papuans are the least genetically diverse.  This study, by not mentioning it at all, seems to disfavor the hypothesis of ancient Papuan/Australasian ancestry in Amazonian populations in South America, although this is a key issue in South American population history that really should have been at least discussed in this paper, even if it couldn't reach a definitive conclusion regarding this point with its own data.

The paper also, implicitly suggests (consistent with prior research), that progenitor modern human populations that left foot prints in New Mexico about 23,000 years ago made only an indiscernible impact, if any, on the primary founding population of the Americas starting around 14,000 years ago. A better discussion of how the genetic profiles of Native American in North America differs from those in South America would also have been welcome. It seems to suggest a somewhat older than conventional population history for the founding population of North America, but does so with little meaningful discussion of North American population genetics.

The lack of data from the Atlantic coast of South America and the very thin data from the Amazon, even compared to prior studies of South American genetics, also suggests to me that it is possible that there could be five rather than four main branches of South American settlement. Even if one can't find "pure" indigenous South American ancestry in this region, it should be possible from large databases of modern populations in this region from prior studies, which is home to a large share of all South Americans, to make strong inferences about it from individuals modern populations in the region with indigenous admixture.

There is also too little discussion of the population genetic impact of the Columbian Exchange on either the main different population groups it infers in South America or on the strength of the inferences it is making. We would expect this event in the last 500 years to cause strong fitness based selection, and possibly hard selective sweeps on HLA genetic diversity, an rate unprecedented in the previous 13,500 years, and HLA genetic diversity is one of the important pieces of data that the study examines. But this question isn't elevated or focused upon by the authors.

Editor’s summary

From our origins in Africa, humans have migrated and settled across the world. Perhaps none of these migrations has been the subject of as much debate as the expansion into and throughout the Americas. Gusareva et al. used 1537 whole-genome sequenced samples from 139 populations in South America and Northeast Eurasia to shed light on the population history of Native Americans. Collected as a part of the GenomeAsia 100K consortium, analysis of these data showed that there are four main ancestral lineages that contributed to modern South Americans. These lineages diverged from each other between 10,000 and 14,000 years ago, and this analysis reveals more details of the population history dynamics in these groups. —Corinne Simonti

Abstract

Genome sequencing of 1537 individuals from 139 ethnic groups reveals the genetic characteristics of understudied populations in North Asia and South America. Our analysis demonstrates that West Siberian ancestry, represented by the Kets and Nenets, contributed to the genetic ancestry of most Siberian populations. West Beringians, including the Koryaks, Inuit, and Luoravetlans, exhibit genetic adaptation to Arctic climate, including medically relevant variants. 

In South America, early migrants split into four groups—Amazonians, Andeans, Chaco Amerindians, and Patagonians—~13,900 years ago. Their longest migration led to population decline, whereas settlement in South America’s diverse environments caused instant spatial isolation, reducing genetic and immunogenic diversity. These findings highlight how population history and environmental pressures shaped the genetic architecture of human populations across North Asia and South America.

Abstract

INTRODUCTION

During the late Pleistocene, humans expanded across Eurasia and eventually migrated to the Americas. Those who reached Patagonia, at the southern tip of South America, completed the longest migration out of Africa.

RATIONALE

The extent of basal divergences, admixture, and degrees of isolation among Indigenous North Eurasian and Native South American populations remain debated, with most insights derived from genome-wide genotyping data. This study aims to deepen our understanding of the ancient dynamics that shaped contemporary populations in North Eurasia and the Americas. By using large-scale whole-genome sequencing of 1537 individuals from 139 ethnic groups in these regions, we examined population structures, elucidated prehistoric migrations, and explored the influence of past environmental factors on the diversification of human populations.

RESULTS

Advances in large-scale genomic sequencing have considerably enhanced our understanding of the genetic ancestry of human populations across North Eurasia and South America. Our analysis reveals that all contemporary Siberians, as well as some Northeast Europeans and Central Asians, share ancestry with the West Siberian groups, represented by the Kets and Nenets. Their ancestors were widespread across Siberia 10,000 years ago (ya), but now these groups face population decline by 73.6% and are becoming a minority.

The populations of west Beringia, including the Koryaks, Inuit, and Luoravetlans, are the most genetically distinct from other Siberians. These groups have adapted to Arctic conditions with genetic variations related to lipid metabolism, thermogenesis, sensory perception, and the regulation of reproductive and immune functions. 

We were not able to identify a specific Siberian group as the direct ancestors of Native Americans owing to deep divergence and limited genetic continuity. However, west Beringian populations remain closely related to Native Americans. Koryaks and Inuit show 5 and 28% Native American ancestry, respectively, owing to gene flow between 700 and 5100 ya.

We estimated the split time of Native South Americas into Amazonians, Andeans, Chaco Amerindians, and Patagonians to have occurred 13,900 to 10,000 ya. Migration and settlement across the continent led to population isolations due to geographic boundaries and a reduction in their genetic diversity, particularly affecting immune genes, such as the human leukocyte antigen (HLA) genes. Over the past 10,000 years, all four Native South American lineages have experienced population declines ranging from 38 to 80%. This dramatic decline, combined with the loss of traditional lifestyles, cultural practices, and languages, has pushed some Indigenous communities, such as the Kawésqar, to the brink of extinction.

CONCLUSION

The migration to an uninhabited continent of South America through the narrow Isthmus of Panama resulted in a founder effect among Native South Americans, leading to reduced genetic diversity compared with that of Indigenous populations of North Eurasia. Over 13,900 years, geographic barriers within the continent further isolated Indigenous groups, subsequently reducing genetic diversity. These groups faced a profound challenge with the arrival of European colonists in the 1600s, who introduced new adversities that threatened their long-standing endurance. 

Genetic ancestry and nucleotide diversity. 

Colors represent genetic ancestries estimated by whole-genome sequencing data of contemporary human populations. Countries having no data remained empty. Circle size indicates the average nucleotide diversity of each population.

Elena S. Gusareva, et al., "From North Asia to South America: Tracing the longest human migration through genomic sequencing" 388 (6748) Science (May 15, 2025) DOI: 10.1126/science.adk5081

The introduction in the body text puts the findings in context:

The late Pleistocene saw the expansion of humans into the frigid lands of Eurasia. The earliest known presence of modern humans in northern Eurasia at latitudes greater than 50°N was around 45,000 years ago (ya) in West Siberia, and by 31,600 ya, humans had migrated far east toward Beringia, north of the Arctic Circle at 71° N. The earliest human remains identified in this region are two Yana Rhinoceros Horn Site individuals that, despite their extreme Northeast Siberian geographical location, show substantial genetic relatedness to early West Eurasian hunter-gatherers. 

The Upper Palaeolithic people who initially populated Northeast Siberia were then replaced by arrivals from East Asia. The Kolyma1 remains, excavated near the Chukotka region and dated as being from 9800 ya, demonstrate greater affinity to East Asians and present-day west Beringian populations, such as Koryaks and Luoravetlans (also known as Chukchi), as well as to Native Americans. The linguistic and cultural diversity of present-day Indigenous Siberian populations is mirrored by the complex patterns of admixture, as shown by genome-wide genotype data analysis. This genetic structure in Siberians, comprising several ancestral components, is estimated to have emerged within the past 10,000 to ~3400 years. The Western Eurasian ancestry component presented in a majority of Indigenous Siberian populations is not the result of postcolonial Russian admixture but one of the ancient components dating back to 12,500 to 25,000 ya in different Siberian populations. Among the present-day populations of Northeast Eurasia, the Koryaks from the Kamchatka Peninsula and the Inuit from Chukotka show the closest genetic relatedness to Native North Americans. 

The migration of humans to the Americas occurred when the Bering Land Bridge was still open, with the earliest human remains in North America found in the Clovis burial site in western Montana dating back to around 12,700 ya. However, recent evidence suggests human presence in North America from at least 23,000 ya. By the time the Ice-Free Corridor opened up and became suitable for travel around 13,300 ya, humans were already widely dispersed in North America, likely owing to Pacific coastal migration routes. The divergence between northern and southern Native American populations is estimated to have occurred between 17,500 and 14,600 ya south of the North American ice sheets, according to modern and ancient genomic analyses. The rapid dispersal of humans in South America is suggested by archaeological records, which date the earliest human presence in North Patagonia, the southernmost tip of the Americas, to 14,500 ya. However, the number of basal divergences, founding populations, admixture, and the degrees of isolation among Native South American populations remain a subject of debate, with most of the current understanding coming from analyses of genome-wide genotyping or ancient DNA data. Additionally, fine-scale population genetic studies based on high-coverage whole-genome sequencing datasets for contemporary populations of North Eurasia and South America have not been performed to date.

The body text's discussion of population decline in South America (which has been continuous and not just entirely due to the Columbian exchange) is notable since rare haplotypes and ancestrally informative genes are strongly prone to being purged in periods of declining population (while happens only rarely in expanding populations). Consistent with this these populations have low genetic diversity.

The population split time estimates also suggest that the divergence of the four Native South American lineages occurred over a short period, from 13,900 to 10,000 ya. All four lineages show a continuous population decline. However, the Andean highlanders managed to maintain their population size during the rise of maize horticulture around 5200 to 3700 ya. It has declined by 45.1% since then (Ne from 1771 to 972), whereas Chaco Amerindians have declined by 46.89% (Ne from 1448 to 769) since 10,000 ya. Amazonians and especially Patagonians have seen a dramatic decrease in population size over the past 10,000 years, with declines of 66.59% (Ne from 1368 to 457) and 79.68% (Ne from 1171 to 238), respectively.

To assess the impact of population decline on genetic diversity, we estimated genome-wide runs of homozygosity (ROHs) segments. In Native South Americans, the average number and length of ROHs segments estimated across all populations were 10.5 and 1.3 times higher than those in Africans (Yoruba) and 3.75 and 1.2 times higher than those in Northeast Europeans, respectively. The highest abundance of extended ROHs was observed in Amazonians, Patagonian Kawésqar, and Chaco Amerindians and was similar to that seen in isolated island populations, such as the Andamanese and Baining. This high homozygosity is likely the result of the founder effect due to long-distance migration and/or population isolation. The strong correlation between the average total number of ROHs and the average nucleotide diversity (Pearson correlation coefficient r = –0.78) supports the idea that the extended homozygosity is a result of population history.

The body text of the discussion section notes that:

Our analysis of whole-genome datasets also allowed us to infer the split time between North Eurasians and Native Americans, which occurred between 26,800 and 19,300 ya. This finding is consistent with estimates based on the recently published paleontological discovery of human footprints in North America (south-central New Mexico) dating back to 23,000 and 21,000 ya, as well as with other genetic studies, despite differences in the cohorts that were investigated. 

A previous study of ancient genomes suggests limited genetic continuity in Beringia, as the most recent Arctic colonization occurred 6000 ya. Therefore, it is likely that the first ancestors of the Native Americans in this region were replaced by the most recent wave of migration. We could not identify a specific Siberian group as direct Native American ancestors among the contemporary Indigenous populations in our dataset. However, we show that west Beringian populations, such as Inuit, Luoravetlans, and Koryaks, are genetically the closest to Native Americans. Moreover, we revealed the gene flow from Native Americans back to Inuit and Koryaks in Chukotka and the Kamchatka Peninsula between 700 to 5100 ya. Our analyses also demonstrated the shared ancestry between the west Beringian populations and contemporary Native North Americans, particularly the Chipewyan from Canada. This genetic relatedness is consistent with the PCA results. These findings are in line with previous reports that describe multiple waves of Northeast Asian gene flow into North Americans, including Neo-Inuit lineages. 

By using our genome sequencing data from diverse Native South Americans, we have discovered that the simultaneous split of the four Native South American ancestral lineages occurred between 13,900 and 10,000 ya from a common ancestral population in Mesoamerica. This rapid radial dispersal and the establishment of sedentary settlements across South America are supported by previous genetic studies and the archaeological findings of early technologies (such as stone tools) that indicate regional cultural diversification in South America from at least 13,000 ya. This divergence occurred shortly after the split of the ancestral Native American lineages into northern and southern branches, which happened between 17,500 and 14,600 ya south of the North American ice sheets. By the time the Ice-Free Corridor was fully opened 14,300 to 13,300 ya during the abrupt warming, humans were already widely dispersed in North America. 

Our study shows that the human migration across South America resulted in population splits with a loss of genetic diversity due to founder effects. Geographical and environmental boundaries caused population isolation and further enhanced the genetic homogenization, similar to islander populations. The demographic history has greatly influenced the Patagonian Kawésqar, whose ancestors migrated the farthest distance out of Africa. They have the smallest effective population size and one of the smallest genetic distances between community members. It has been reported that contemporary Native Patagonians (including the Kawésqar) show the highest genetic affinity to ancient Patagonian maritime individuals that lived 1000 ya, indicating genetic continuity in the region. Our study cannot provide evidence for the reported back migration from the Southern Cone along South America's Atlantic coast owing to a lack of data on east coastal Native South American populations. 

Our study also suggests that close genetic relatedness in Indigenous populations, along with reduced heterozygosity in HLA genes, may impact antigen recognition ability to new unexposed pathogens. In combination with socioeconomic factors and limited access to medical care, this could pose a potential health risk. High–pathogen load regions, such as Southeast Asia, tend to have a higher diversity of promiscuous HLA-DRB1 alleles, which allows them to respond to a wider range of extracellular pathogens. However, emerging evidence that divergent allele advantage (a mechanism where the HLA genotypes present a broader set of epitopes) and increase in HLA alleles promiscuity level may counterplay the effect of loss of heterozygosity in HLA genes. Our work highlights a noteworthy implication for future research in population-based disease cohorts: Epitope-binding repertoire studies are essential for identifying the dynamic effects of limited HLA diversity on disease susceptibility. 

Access to the vastness of the South American continent was constrained by the relatively small landmass of the Isthmus of Panama. Consequently, migrating groups could only inhabit the continent from a singular direction, limiting the genetic diversity of human individuals. This ultimately led to the emergence of the four ancestries described in our analysis. Although Indigenous groups managed to maintain their populations for over 13 millennia with minimal interaction with other groups, their endurance faced a critical challenge with the arrival of the initial colonists in the 1600s.

Proteins In Hominin Fossil In Taiwan Are Denisovan

While the jaw bone still isn't enough to develop much of an image of what Denisovans looked like, this is definitely a major, although not unexpected, development. Denisovan admixture in modern humans had already strongly suggested a broad range for them in Asia, even though this is the first definitively identified Denisovan bone sample from comparatively warm regions in southern Asia.

A fossilized jawbone found off the coast of Taiwan more than 20 years ago belonged to a group of ancient humans, called the Denisovans, first identified in a Siberian cave.

The finding, published today in Science1, is the result of time-consuming work to extract ancient proteins from the fossil. It also expands the known geographical range of the group, from colder, high-altitude regions to warmer climates.

“I’m very excited to see this,” says Janet Kelso, a computational biologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The lower jawbone, with four teeth intact, is called Penghu 1 and was dredged up by fishing crews from the Penghu channel, 25 kilometres off the west coast of Taiwan. Penghu 1 was donated to Taiwan’s National Museum of Natural Science in Taichung after researchers recognized its significance as coming from an ancient human relative2. But the identity of that unknown relative remained a mystery, until now.

Ancient proteins

Researchers spent more than two years carefully refining techniques for extracting ancient proteins from animal bones taken from the channel. They then used acid to isolate protein fragments from the surface of a Penghu 1 molar tooth and enzymes to extract them from the jawbone.

The team identified several degraded fragments, two of which bore specific amino-acid sequence variations matching those seen in the genetic sequences of a Denisovan finger bone3 found in the Denisova Cave in southern Siberia in 2008. The researchers could also tell that the jawbone came from a male Denisovan.

It’s the second location that molecular evidence from ancient proteins has definitively linked fossil remains to the Denisovans. The first was in a cave in Xiahe, Tibet where proteins from a jawbone4 and then a rib bone were determined to be from Denisovans.

Pinning down an exact age for the Penghu fossil is challenging because scientists do not have samples of the sediment it was buried in.

“One can only say it’s older than 50,000” years, says Rainer Grün, a geochronologist at the Australian National University in Canberra, who dated the fossil in 2015 and subsequently reanalysed the data5.

The Xiahe 1 mandible is at least 160,000 years old, and material from the Denisova cave indicates that Denisovans lived in Siberia between 200,000 and 50,000 years ago. At that time, sea levels were lower and the Chinese mainland was connected to Taiwan.

From here. 

The paper and its abstract are as follows:

Editor’s summary

Denisovans are a Pleistocene hominin lineage first identified genomically and known from only a few fossils. Although genomic studies suggest that they were widespread throughout Asia, fossils of this group have thus far only been identified from regions with cold climates, Siberia and Tibet. 

Tsutaya et al. used ancient proteomic analysis on a previously unidentified hominin mandible from Taiwan and identified it as having belonged to a male Denisovan. This identification confirms previous genomic predictions of the group’s widespread occurrence, including in warmer climates. The robust nature of this mandible is similar to that seen in a Denisovan one from Tibet, suggesting that this is a consistent trait for the lineage. —Sacha Vignieri

Abstract

Denisovans are an extinct hominin group defined by ancient genomes of Middle to Late Pleistocene fossils from southern Siberia. Although genomic evidence suggests their widespread distribution throughout eastern Asia and possibly Oceania, so far only a few fossils from the Altai and Tibet are confidently identified molecularly as Denisovan. 

We identified a hominin mandible (Penghu 1) from Taiwan (10,000 to 70,000 years ago or 130,000 to 190,000 years ago) as belonging to a male Denisovan by applying ancient protein analysis. We retrieved 4241 amino acid residues and identified two Denisovan-specific variants. The increased fossil sample of Denisovans demonstrates their wider distribution, including warm and humid regions, as well as their shared distinct robust dentognathic traits that markedly contrast with their sister group, Neanderthals.

Takumi Tsutaya, et al., "A male Denisovan mandible from Pleistocene Taiwan" 388 (6743) Science 176-180 (April 11, 2025). Hat tip to Neo in the comments.

Did Homo Sapiens Arise As A Hybrid?

In addition to being highly model dependent and unsupported by ancient DNA data, and hence somewhat speculative, this is really a less revolutionary proposal than it seems. 

Modern humans still arise in Africa (including a hypothetical admixture event that gives rise to the new species ca. 290,000 years ago). Basically, it is just proposing that in addition to the Neanderthal admixture shared by all non-Africans, and the Denisovan admixture that took place in the first generation of modern humans to reach Asia, there was an 20% admixture event from Homo erectus involving all modern humans associated with the emergence of the new species.

In their model, the 80% source, probably Homo heidelbergensis is also ancestral to Neanderthals and Denisovans, evolves from from Homo erectus about 1,500,000 years ago and suffers a severe bottleneck period, while the 20% Homo erectus ancestry was exclusive to Homo sapiens and was probably initially a larger percentage as a result of an admixture event in Africa about 290,000 years ago. The Homo erectus ancestry percentage was reduced in percentage over time due to its inferior selective fitness in most parts of the Homo erectus genome that have an impact on phenotypes (i.e. that have any actual discernible effect).

The evolutionary path leading to the rise of modern humans is full of twists and turns, and the latest surprise reveals that our species likely sprung forth from two ancient intermingling populations. A new study has confirmed that these groups first diverged from each other around 1.5 million years ago and later merged back together 300,000 years ago, initiating a genetic mixing event that culminated with the birth of modern humans.

The study, published in Nature Genetics, completely rewrites the story of humans. Scientists have long believed that Homo sapiens first appeared in Africa somewhere between 200,000 years and 300,000 years ago, having descended from a single ancestral lineage. The idea of genetic admixture flips the script, however, showing that human origins are much more complex than previously thought.

The researchers . . . tapped into modern human DNA from the 1000 Genomes Project, an international catalog filled with human genomes from a variety of populations. The research team created a computational algorithm called cobraa, which was designed to represent the event of an ancestral population splitting and rejoining. . . . 

With this method, they were able to produce a structured model that displayed two ancestral populations breaking apart in ancient times. In the years after this divergence, one of the populations experienced major fluctuations in size.

“Immediately after the two ancestral populations split, we see a severe bottleneck in one of them — suggesting it shrank to a very small size before slowly growing over a period of one million years,” said co-author Aylwyn Scally from the University of Cambridge’s Department of Genetics, in a statement. “This population would later contribute about 80 percent of the genetic material of modern humans and also seems to have been the ancestral population from which Neanderthals and Denisovans diverged.”

The second population, meanwhile, contributed 20 percent to the genetic makeup of modern humans. The researchers found that many of the genes this group passed along to humans were not located near regions of the genome corresponding to gene functions; this could reflect a concept called purifying selection, which is the process of natural selection filtering out harmful mutations. However, the researchers believe that some of the genes from the second population may have still been integral to brain development in modern humans.  . . .

An element of mystery still surrounds the identity of these ancestral populations. The researchers point to Homo erectus and Homo heidelbergensis as potential answers since they were present in Africa around the time of the genetic admixture, but further research is needed to match genetic ancestors with fossil groups.

Nature Genetics. A structured coalescent model reveals deep ancestral structure shared by all modern humans

From Discover Magazine. The abstract of the open access paper states:

Understanding the history of admixture events and population size changes leading to modern humans is central to human evolutionary genetics. Here we introduce a coalescence-based hidden Markov model, cobraa, that explicitly represents an ancestral population split and rejoin, and demonstrate its application on simulated and real data across multiple species. 

Using cobraa, we present evidence for an extended period of structure in the history of all modern humans, in which two ancestral populations that diverged ~1.5 million years ago came together in an admixture event ~300 thousand years ago, in a ratio of ~80:20%. Immediately after their divergence, we detect a strong bottleneck in the major ancestral population. 

We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background. Moreover, we found a strong correlation between regions of majority ancestry and human–Neanderthal or human–Denisovan divergence, suggesting the majority population was also ancestral to those archaic humans.

Why Do We Kiss?

Why do we kiss? Is there an evolutionary advantage to it? This article tries to answer that question.

A kiss has been a signal of special affection across continents and cultures for millennia. Between times and peoples, social norms invariably prescribe kissing to specific affiliations and contexts, implying deeper biological bases. Why the protruding of the lips and slight suction when touching another? 

Capuchin monkeys stick their fingers in their friends' eyes as sign of affection, why have humans developed kissing? 

Here I briefly review proposed hypotheses for the evolution of human kissing. Great ape social behavior suggests that kissing is likely the conserved final mouth-contact stage of a grooming bout when the groomer sucks with protruded lips the fur or skin of the groomed to latch on debris or a parasite. The hygienic relevance of grooming decreased over human evolution due to fur-loss, but shorter sessions would have predictably retained a final “kissing” stage, ultimately, remaining the only vestige of a once ritualistic behavior for signaling and strengthening social and kinship ties in an ancestral ape.

Adriano R. Lameira, "The evolutionary origin of human kissing" Evolutionary Anthropology (October 17, 2024) https://doi.org/10.1002/evan.22050

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).