While I have been relatively off-line, regular commenter John B has been emailing me material. It now seems an appropriate point to bring that material on line. The long post that follows reports on three recent studies, concluding with a short discussion. My continued indebtedness to John B will be apparent.
Homo Luzonensis
The map from the paper is shown, including land that would have been revealed at various sea levels below the present. The abstract from the paper is set out below.
"A hominin third metatarsal discovered in 2007 in Callao Cave (Northern Luzon, the Philippines) and dated to 67 thousand years ago provided the earliest direct evidence of a human presence in the Philippines. Analysis of this foot bone suggested that it belonged to the genus Homo, but to which species was unclear. Here we report the discovery of twelve additional hominin elements that represent at least three individuals that were found in the same stratigraphic layer of Callao Cave as the previously discovered metatarsal. These specimens display a combination of primitive and derived morphological features that is different from the combination of features found in other species in the genus Homo (including Homo floresiensis and Homo sapiens) and warrants their attribution to a new species, which we name Homo luzonensis. The presence of another and previously unknown hominin species east of the Wallace Line during the Late Pleistocene epoch underscores the importance of island Southeast Asia in the evolution of the genus Homo."
Florent Détroit, Armand Salvador Mijares, Julien Corny, Guillaume Daver, Clément Zanolli, Eusebio Dizon, Emil Robles, Rainer Grün & Philip J. Piper, A new species of Homo from the Late Pleistocene of the Philippines, Nature volume 568, pages 181–186 (2019) Published on-line 10 April 2019, accessed 22 October 2019
The BBC article as well as other commentary quotes Professor Chris Stringer, from London's Natural History Museum. For those who follow Twitter, Professor Stringer is an active tweeter - @ChrisStringer65.
John kindly sent me a press release apparently issued by Professor Stringer at the time. This is set out below. I have not been able to find a link to the original but have included it in full because of the overview it provides.
"Homo Luzonensis - a new human species from island south east Asia
After the remarkable finds of the diminutive Homo floriensis were published in 2004, I said that the experiment in human evolution conducted on Flores could have been repeated on many of the other islands in the region. That speculation has seemingly been confirmed on the island of Luzon in the Philippines, nearly 3,000 km away. 13 fossil human remains - teeth, hand and foot bones, and part of a femur from at least 3 adults and immature individuals have been recovered from excavations at Callao Cave since 2007. They have been dated to at least 50,000 years old, are small in size, particularly the teeth, and they show a distinctive combination of primitive and and derived traits sufficient for the authors of the paper in Nature to create a new human species for them: Homo luzonensis. They suggest that some of the hand and foot bones show features also present in much more ancient australopiths ("southern apes") found in Africa, and interpreted as adaptations for life in the trees.
So, do these finds really represent a new species, and what do they add to the story of human evolution? Given the small size of the sample, some scientists will question the wisdom of creating a new species based on such limited material, while others such as me wonder whether Luzon find might eventually turn out to be a variant of the already known Homo floresiensis, despite some clear differences. And we know that island isolation can be a catalyst for some odd evolutionary changes, including reversion to apparently primitive states. Nevertheless, for the moment, it is probably reasonable to accept the new species, at least provisionally, while awaiting more finds.
As for its origins and fate, they remain mysterious. As with floresiensis, expert opinion will probably be divided. Some will argue that the primitive features of luzonensis are evidence of a pre- Homo erectus dispersal out of Africa, perhaps more than 2 million years ago. floresiensis and luzonensis would represent some of the last survivors of that early wave, lingering on at the fringes of the inhabited world. Others would prefer to regard these island forms as descendants of Homo erectus, subject to isolation and island dwarfing over a considerable period of time. And given two such populations in the remote islands of south east Asia, others like me might consider they represent remnants of a dispersal of an original floresiensis or luzonensis -like founder lineage that originated somewhere like the island of Sulawesi. As for the fate of luzonensis, it is too early to say whether the spread of Homo sapiens into the region at least 50,000 years ago might have been factor in its disappearance, as has been suggested for floresiensis.
An extra layer of complexity in the region has been added by recent research on the Denisovans, an archaic population of humans originally identified from ancient DNA recovered from human fossils in Denisova Cave, Siberia. The additional existence of late Denisovan-like populations in south east Asia had been inferred from the presence of related DNA in extant Asian and Oceanian people, but recent research indicates at least three separate and varied Denisovan-like sources, at least one of which probably lived in the same wide biogeographic zone as floresiensis and luzonensis. We are currently far from establishing which fossils in the region might represent such populations, but it is probable that the spread of Denisovan-like people into the region was a separate and much later event than those involving floresiensis and luzonensis." Ends
Another who commented on the Luzon discoveries was Professor John Hawks. His New species of hominin from Luzon appeared on his blog on 10 April 2019 and in the online journal Sapiens at the same time. It covers some of the same ground as Professor Stringer's comment, but with more focus on the details of the evidence.
Multiple Deeply Divergent Denisovan-related ancestries in Papuans
At the same time as the Luzonensis results were reported, another paper was released in Cell entitled Multiple Deeply Divergent Denisovan-related ancestries in Papuans.
The abstract reads:
"Genome sequences are known for two archaic hominins-Neanderthals and Denisovans-which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time."On 11 April, EuekaAlert carried a press release from the Max Planck Institute for Evolutionary Anthropology. I have set this out below in full because it provides another perspective.
Jacobs GS, Hudjashov G, Saag L, Kusuma P, Darusallam CC, Lawson D, Mondal M, Pagani L, Ricaut FX, Stoneking M, Metspalu M, Sudoyo H, Lansing JS, Cox MP, Multiple Deeply Divergent Denisovan-related ancestries in Papuans, Cell. 2019 May 2;177(4):1010-1021.e32. doi: 10.1016/j.cell.2019.02.035. Epub 2019 Apr 11.Accessed 23 October 2019
"Multiple Denisovan-related ancestries in Papuans
DNA sequences from Indonesia and New Guinea reveal new branches of the Denisovan family tree
The findings are based on a new study led by Murray Cox from Massey University in New Zealand and made possible by sampling efforts led by Herawati Sudoyo from the Eijkman Institute for Molecular Biology in Jakarta, Indonesia. The data were collected and analyzed by an international team of researchers, including Mark Stoneking from the Max Planck Institute for Evolutionary Anthropology. Taken together with previous work - which has pointed to a third Denisovan lineage in the genomes of modern Siberians, Native Americans, and East Asians - the evidence "suggests that modern humans interbred with multiple Denisovan populations, which were geographically isolated from each other over deep evolutionary time," the researchers write.
The new evidence also unexpectedly shows extra mixing between Papuans and one of the two Denisovan groups, suggesting that this group actually lived in New Guinea or its adjacent islands. Moreover, Denisovans may have lived in the area until as recently as 30,000 years ago, making them one of the last surviving groups of archaic hominins. "People used to think that Denisovans lived on the Asian mainland and far to the north," says Cox. "Our work instead shows that the center of archaic diversity was not in Europe or the frozen north, but instead in tropical Asia." Stoneking adds, "Moreover, this archaic diversity seems to have persisted much longer in Island Southeast Asia and New Guinea than elsewhere in the world."
It had already been clear that Island Southeast Asia and New Guinea was a special place, with individuals there carrying more archaic hominin DNA than anywhere else on Earth. The region was also recognized as key to the early evolution of Homo sapiens outside Africa. But there were gaps in the story.
Divergent Denisovan lineages
To help fill those gaps, the team identified stretches of archaic DNA from 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea. Their analyses uncovered large stretches of DNA that did not jibe with a single introgression of genes from Denisovans into humans in the region. Instead, they report, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages. In fact, they estimate that those two groups of Denisovans had been separated from one another for 350,000 years.
The new findings highlight how "incredibly understudied" this part of the world has been, the researchers say. To put it in context, many of the study's participants live in Indonesia, a country the size of Europe that is the 4th largest country in the world based on population size. And yet, apart from a handful of genome sequences reported in a global survey of genomic diversity in 2016, the new paper reports the first Indonesian genome sequences. There also has been a strong bias in studies of archaic hominins toward Europe and northern Eurasia, because DNA collected from ancient bones survives best in the cold north.
Missing data bias scientific interpretation
This lack of global representation in both ancient and modern genome data is well noted, the researchers say. "However, we don't think that people have really grasped just how much of a bias this puts on scientific interpretations - such as, here, the geographical distribution of archaic hominin populations," Cox says.
As fascinating as these new findings are, the researchers say their primary aim is to use this new genomic data to help improve healthcare for people in Island Southeast Asia. They say this first genome survey in the region now offers the baseline information needed to set that work in motion." Ends
Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes
On 18 October 2019, Science published another study under the catchy (!) title Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes. The above graphic reproduced from the article provides an effective schematic.
In this case, I am not providing the full abstract (you will find it here) because of length as well as complexity. However, a short extract follows:
"Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation."Discussion
PingHsun Hsieh, Mitchell R. Vollger, Vy Dang, David Porubsky, Carl Baker, Stuart Cantsilieris, Kendra Hoekzema1, Alexandra P. Lewis, Katherine M. Munson, Melanie Sorensen, Zev N. Kronenberg, Shwetha Murali, Bradley J. Nelson1, Giorgia Chiatante, Flavia Angela Maria Maggiolini, Hélène Blanché, Jason G. Underwood, Francesca Antonacci, Jean-François Deleuze, Evan E. Eichler, Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes, Science 18 Oct 2019:Vol. 366, Issue 6463, eaax2083 DOI: 10.1126/science.aax2083, accessed 22 October 2019
In sending me material, John B commented (24 April 2019): "It is increasingly looking likely Jim that the Aboriginals who first colonised Australia were locals to the region and not in transit through it, my suspicions of the original Out of Africa single origin hypothesis, replacement hypothesis, or recent African origin model continue to be confirmed. Archaic diversity, I do like that descriptor and the picture it conveys."
John and I have been talking about these issues now for a number of years. Over that time, new research discoveries have added to our understanding, but also created an unexpectedly complex and uncertain picture.
In 2017, reports of results from the excavations at the Madjedbebe rock shelter, The lessons and questions from Madjedbebe, pushed back the date of human occupation of Northern Australia to perhaps 65,000. I was going to write Aboriginal occupation but, while it seems probable, we don't actually know that the continent of Sahul was first occupied by the descendants of today's Aboriginal Australians.
In October 2016 in a paper entitled A genomic history of Aboriginal Australia, by Anna-Sapfo Malvinas, Michael C Westerway et all, the authors concluded that:
I will leave aside the last conclusion for it raises another set of issues that is important to the history of Aboriginal Australia but is outside the scope of this post.
At the time, the estimate of 51–72 kya for divergence from Eurasians following a single out-of-Africa dispersal made me uncomfortable because the archaeological evidence was already suggesting possible early dates for human occupation of Sahul that might possibly conflict with these time lines. The Madjedbebe results added to this discomfort: the suggested 65,000 years was remarkably close to the suggested 72kya out of Africa date.
Before going on, I note that all the dating techniques involve statistical analysis with confidence intervals. Apparent differences and inconsistencies may reflect no more than this.
The latest discoveries covered in this blog post suggest that:
In writing to me, John also noted:
"I have just been reading a Geology paper that mentioned the super volcano Toba eruption as the largest single event of its type so far known. It struck me that this could have been the event to precipitate human migration into Australia. We now understand that the arrival of H.sapiens into Oz occurred most likely as a bulk entry over a very short period then nobody else over millennia. Could Toba have been the push factor ?"
I am not convinced that there was a single pulse and am generally sceptical of attributions to volcanic eruptions. But still. As dates get pushed back, the possibility that the Toba eruption played a role in the movement of and ending of human species becomes more plausible!
In 2017, reports of results from the excavations at the Madjedbebe rock shelter, The lessons and questions from Madjedbebe, pushed back the date of human occupation of Northern Australia to perhaps 65,000. I was going to write Aboriginal occupation but, while it seems probable, we don't actually know that the continent of Sahul was first occupied by the descendants of today's Aboriginal Australians.
In October 2016 in a paper entitled A genomic history of Aboriginal Australia, by Anna-Sapfo Malvinas, Michael C Westerway et all, the authors concluded that:
- Aboriginal Australians and Papuans diverged from Eurasians and estimate 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations
- Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya
- We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages.
I will leave aside the last conclusion for it raises another set of issues that is important to the history of Aboriginal Australia but is outside the scope of this post.
At the time, the estimate of 51–72 kya for divergence from Eurasians following a single out-of-Africa dispersal made me uncomfortable because the archaeological evidence was already suggesting possible early dates for human occupation of Sahul that might possibly conflict with these time lines. The Madjedbebe results added to this discomfort: the suggested 65,000 years was remarkably close to the suggested 72kya out of Africa date.
Before going on, I note that all the dating techniques involve statistical analysis with confidence intervals. Apparent differences and inconsistencies may reflect no more than this.
The latest discoveries covered in this blog post suggest that:
- Earlier hominum species were in South East Asia long before modern humans
- Those species had come in different waves and had diversified
- Those species had crossed the Wallace Line, overcoming sea barriers. They may even have reached Sahul
- Those species and modern humans overlapped far more than previously realised, co-existing in various forms of relationships including inter-breeding
- Aboriginal and Papuan groups that formed the basis of later population may have lived in what is now SE Asian for extended periods before moving on, not just passing through.
In writing to me, John also noted:
"I have just been reading a Geology paper that mentioned the super volcano Toba eruption as the largest single event of its type so far known. It struck me that this could have been the event to precipitate human migration into Australia. We now understand that the arrival of H.sapiens into Oz occurred most likely as a bulk entry over a very short period then nobody else over millennia. Could Toba have been the push factor ?"
I am not convinced that there was a single pulse and am generally sceptical of attributions to volcanic eruptions. But still. As dates get pushed back, the possibility that the Toba eruption played a role in the movement of and ending of human species becomes more plausible!
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