Patagonian monsters: 2020

Tuesday, December 15, 2020

130ky Cerutti site stone tools validated as made by human beings?

In April 2017 we posted about the Cerutti mastodon site in California, with its "stone tools" dated to 130,000 years ago.

An article (Raman and optical microscopy of bone micro-residues on cobbles from the Cerutti mastodon site) published this month, reports finding bone micro residues on the cobbles found next to the broken mastodon bones, suggesting that these were used as tools to break the bones open and not just a chance accumulation of stones and broken bones.

The abstract states:

"Cobbles from the Cerutti Mastodon (CM) site have impact marks and usewear suggesting that mastodon bones were placed on stone anvils and struck with stone hammers to produce two concentrations of broken bones and stones. Critics have suggested that the stones may have broken by rolling down slopes rather than in situ at the two concentrations. Our analysis of two cobbles (pegmatite CM-254 and andesite CM-281) identifies bone micro-residues that are not evenly distributed over the cobbles, and are unlikely to have been transferred from sediment or from passive contact with adjacent macro-bones. Bone micro-residues on cobble CM-254 were recovered from surfaces associated with usewear, but were absent from the naturally broken surface found in direct contact with a mastodon rib. In addition, bone micro-residues on cobble CM-281 were recovered from upward facing locations with impact marks and other usewear; but were absent on the downward facing surface. Bone micro-residues are absent in sediment away from the bone concentrations. These new data support the argument that the associated concentration of broken stones and mastodon bones is in situ, and that bones in this concentration were likely broken by the pegmatite cobble (comprising CM-254 and other fragments), when it struck mastodon bones placed on the andesite cobble CM-281. These findings add to the totality of evidence that supports human agency rather than geological processes as the driver responsible for the CM taphonomic pattern. "

Saturday, December 5, 2020

Archaic admixture into Africans

The article I mention in this post was published in Feb. 2020 (Recovering signals of ghost archaic introgression in African populations by Sriram Sankararaman and Arun Durvasula Science Advances 12 Feb 2020:Vol. 6, no. 7, eaax5097 DOI: 10.1126/sciadv.aax5097). It reports an " archaic introgression into four West African populations. Our analyses ... indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans".

The authors "estimate that the archaic population split from the ancestor of Neanderthals and modern humans 360 thousand years (ka) to 1.02 million years (Ma) B.P. and subsequently introgressed into the ancestors of present-day Africans 0 to 124 ka B.P. contributing 2 to 19% of their ancestry."

Could African "diversity" often used to justify the continent as the cradle of mankind be due to this introgression?

Sunday, September 27, 2020

The Y chromosome of Neanderthals

A paper published in Science (The evolutionary history of Neanderthal and Denisovan Y chromosomes by Martin Petr et al. SCIENCE 25 SEP 2020 : 1653-1656), reports that "interbreeding between early humans and Neanderthals and selection replaced the more ancient Denisovian-like Y chromosome and mitochondria in Neanderthals".

The paper includes this tree:

Caption for image: "A) Neighbor-joining tree estimated from the Y chromosome genotype calls, excluding C-to-T and G-to-A polymorphisms, rooted with a chimpanzee as the outgroup (14). Numbers show bootstrap support out of 100 bootstrap replicates. Terminal branch lengths are not informative about the ages of specimens (Fig. 1A), owing to differences in sequence quality. (B) Estimates of TMRCA between Y chromosomes along the x axis and a panel of 13 non-African Y chromosomes. Each dot represents the TMRCA with a single non-African Y chromosome, with error bars showing 95% CI from a resampling of branch counts (14). Black horizontal lines show the mean TMRCA calculated across the full non-African panel (dashed lines) with resampling-based 95% CI (solid lines) (14).".

I have written about Neanderthal Y chromosome in two posts (May 2014 and May 2018), so I found this paper really intersting.

It suggest that:

Denisovans, Neanderthals and Humans lie on three separate phylogentic branches ("the Denisovan Y chromosomes form a separate lineage that split before Neanderthal and modern human Y chromosomes diverged from each other (Fig. 2A). Notably, all three late Neanderthal Y chromosomes cluster together and fall outside of the variation of present-day human Y chromosomes"). This is what one would expect.
Split dates: "The two Denisovan Y chromosomes split from the modern human lineage around 700 ka ago ... By contrast, the three Neanderthal Y chromosomes split from the modern human lineage about 370 ka ago". Which also seems quite normal to me.
They conclude that "The Denisovan–modern human Y chromosome TMRCA estimates agree with population split times inferred from autosomal sequences, suggesting that the differentiation of Denisovan Y chromosomes from modern humans occurred through a simple population split"
And find the 370 ky TMRCA too recent for the Neanderthal Y chromosome. They authors write: "By contrast, the young TMRCA of Neanderthal and modern human Y chromosomes and mtDNAs suggest that these loci have been replaced in Neanderthals through gene flow from an early lineage closely related to modern humans."

So they concluded that a line of modern humans admixed into Neandethals, and they completely replaced Neanderthal Y chromosomes and that is why the split seems so recent. Instead of reflecting the older age they expected. This is summarized as "Autosomal genomes show that Neanderthals and Denisovans are sister groups that split from modern humans between 550 thousand and 765 thousand years (ka) ago. By contrast, the mtDNAs of Neanderthals and modern humans are more similar to one another [time to the most recent common ancestor (TMRCA) of 360 to 468 ka ago] than to the mtDNAs of Denisovans."

They add: "We conclude that the Y chromosomes of late Neandertals represent an extinct lineage closely related to modern human Y chromosomes that introgressed into Neanderthals between ~370 and ~100 ka ago. The presence of this Y chromosome lineage in all late Neanderthals makes it unlikely that genetic changes that accumulated in Neanderthal and modern human Y chromosomes before the introgression led to incompatibilities between these groups".

Now, they only sampled 3 male Neanderthals. Perhaps a larger sample may result in a different outcome. An introgression 370 ka would mean that these humans "closely related" modern humans left Africa -assuming the Out Of Africa theory is correct- 370 ka in an ancient migration and mated with Neanderthals. Since their Y chromosome is distinct from ours, these "closely related" people must have died out in Eurasia.

But looking at the tree and the dates, why conclude an admixture from "closely related" humans into Neanderthals? An admixture that erased old Neanderthal Y chromosomes?

Occam's razor approach suggests: the Neanderthals have a different Y chromosome to us and to Denisovans (fig. above, B) it lies on a different branch. Which ratifies the conclusion. So is the age an issue? 370 ka is too recent?

Why not look into the assumptions that lead to this date? Such as the mutation rate (they estimated 7.34 × 10⁻¹⁰ per base pair per year) or the age they adopted for the "oldest Y lineages" (A00): ~249 ka ago.

I am agree with the authors when they state " Furthermore, we predict that the ~400-ka-old Sima de los Huesos Neanderthals should carry a Y chromosome lineage more similar to that of Denisovans than to that of later Neanderthals", it is reasonable, and does not impact on their supposed Y chromosome replacement theory. Sima de los Huesos chromosomes may also have evolved into what we find in later Neanderthals.

Wednesday, September 16, 2020

Ancient H. erectus introgression into Denisovans and Neanderthals

A recent paper used statistical tools to look into ancient introgressions in the modern human line. The authors reported in their abastract that "We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these “super-archaic” regions—comprising at least about 4Mb—were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.".

You can read the full text of the paper here (Hubisz MJ, Williams AL, Siepel A (2020) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet 16(8): e1008895. https://doi.org/10.1371/journal.pgen.1008895).

Some higlights:

The program they used "calls nearly 0.5% introgression from the Neanderthal into each of the African individuals. These calls are likely explained by a combination of false positives and back-migration into Africa from Europe. However, another possibility is that some regions introgressed into Neanderthals from ancient humans may be assigned the wrong direction". So they did find Neanderthal introgression in Africans but seem to write it off as a fabricaton of the program or false positives, and maybe back-migration.
"We identify 1% of the Denisovan genome as introgressed from a super-archaic hominin—roughly double the estimated false positive rate (0.49%) for this event. Our apparent weak power for these events (another group has estimated ∼6% introgression) suggests that the super-archaic divergence may have been somewhat recent (perhaps closer to 1Mya than 1.5Mya). Still, this analysis resulted in 27Mb of sequence that may represent a partial genome sequence from a previously unsequenced archaic hominin. In addition, ARGweaver-D predicted that a small fraction of the Neanderthal genomes is introgressed from a super-archaic hominin (0.75% for Altai and 0.70% for Vindija), an event that has not been previously hypothesized. However, these fractions only slightly exceed the estimated false positive rate (0.65%), so these results are likely dominated by spurious predictions."
This is indeed interesting. The time frame means surely an introgression from Homo erectus into Denisovans, in Asia. And also a probable admixture of H. erecrtus with Neanderthals!
The introgression between the super-archaic into Denisovans was relatively recent: "...suggests that tmig > 225kya for the for the Sup→Den event"
"our analysis suggests that at least about 4Mb of modern human genomes derives from an unknown but highly diverged archaic hominin, possibly Homo erectus, through at least two separate introgression events".
The authors validate an early admixture of Humans into Neanderthals in Asia some 200 to 300 kya: "Our follow-up analysis based on the frequencies of introgressed elements among the two diploid Neanderthal genomes suggests that the Hum→Nea gene flow occurred roughly between 200 and 300kya, within the limits of accuracy imposed by our assumed demographic model, mutation rates, and generation time. As previously noted, because contact between modern humans and Neanderthals most likely took place in Eurasia, this timeline appears to be inconsistent with a genetic exchange involving the direct ancestors of most present-day Eurasians, who migrated out of Africa ∼50kya. Instead, our timeline suggests an earlier migration, occurring at least 200kya.". Yet they assume (without explaining why) that "These early migrating humans may later have gone extinct, leaving a genetic trace only in introgressed segments in Neanderthals."
They "only detected a low rate of Sup→Afr introgression, somewhat below our estimated false positive rate." which is attributed to using a large population size, based on the assumption of their model -Africa as cradle of mankind had the largest population size.
On ancient introgressions: "It is plausible that if Homo erectus mixed with the Denisovans, they may have also mixed with Neanderthals, perhaps in the Middle East; or perhaps DNA passed from Homo erectus to Neanderthal through the Denisovans. Altogether, given the number of gene flow events now documented among ancient hominins, it may be reasonable to assume that genetic exchange was likely whenever two groups overlapped in time and space."
The authors did not discriminate between Africans and Non-Africans in this study: "When analyzing non-African humans, we only included the “recent” migration bands from Neanderthals and Denisovans into humans, whereas when looking for older introgression events, we excluded the “recent” bands as well as non-African humans. Throughout this paper, all humans are placed in the same population; we do not model divergences within human populations... on this time scale, the European/African split is very recent, so that we did not model the population divergence among modern humans or recent growth in out-of-Africa populations".

Saturday, July 25, 2020

H. luzonensis and H. floresiensis possible link to Denisovans

Just a brief post to share a paper published yesterday (Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia Joao C Teixeira, Guy S Jacobs, Chris Stringer, Jonathan Tuke, Georgi Hudjashov, Gludhug A Purnomo, Herawati Sudoyo, Murray P Cox, Ray Tobler, Chris SM Turney, Alan Cooper, Kristofer M Helgen bioRxiv 2020.07.24.219048; doi: https://doi.org/10.1101/2020.07.24.219048).

The authors were looking into the "super-archaic" hominins that were discovered in the Island Southeast Asia (ISEA) region: Homo luzonensis and H. floresiensis, which were contemporary to anatomically modern humans (AMH). As modern populations in the region have a high level of Denisovan introgression they wanted to find out if there was also a signal of introgression from the super-archaics in the region.

Their analysis failed to detect super-archaic admixture but they reached an interesting conclusion:

"An alternative explanation is that H. luzonensis and H. floresiensis belong to a hominin clade that is considerably less divergent from AMH than is currently accepted, possibly being the latesurviving descendants of an earlier radiation of a Denisovan-like lineage across ISEA.
This would imply that hominin occupation of Flores (1.2Ma) and the Philippines (700ka) was not continuous and that the ubiquitous Denisovan ancestry across ISEA, which includes signals of admixture from a Denisovan population that diverged from the Altai Denisovans ~280ka, results from AMH admixture with one or both of these groups.
Indeed, the patterning of Denisovan ancestry across ISEA is consistent with separate Denisovan introgression events in the Philippines and, potentially, in Flores. Despite the complete lack of support for this scenario from current morphological interpretations, it is possible that pronounced dwarfism and prolonged periods of endemic island evolution for H. floresiensis and H. luzonensis complicate morphological assessments and phylogenetic placement of these groups.
While it would simplify the search for ‘southern Denisovans’ if they could be linked with the dwarfed hominins of Flores and Luzon, existing archaeological and morphological data and Flores as a more likely location for the sources of Denisovan-like DNA."

Below a map of the sites where Denisovan, Flores and Luzon hominins' remains were found:

Could the Denisovans be a link to the Homo erectus population of Asia? Current research links them to Neandertals in western Eurasia.

Thursday, July 23, 2020

Chiquihuite Cave occupied 35,000 years ago? A very early date for human presence in America

This paper, published in Nature yesterday: Ardelean, C.F., Becerra-Valdivia, L., Pedersen, M.W. et al. Evidence of human occupation in Mexico around the Last Glacial Maximum. Nature (2020). https://doi.org/10.1038/s41586-020-2509-0, found evidence that human beings lived in the Chiquihuite Cave for around 20,000 years, starting some 35 ky ago.

The cave is located in north central Mexico (see map) in a dry area, which at the time had forests that resembled those we now see in British Columbia or NW USA.

The authors unearthed stone tools in the cave but these are quite unusual: "The site yielded about 1,900 stone artefacts within a 3-m-deep stratified sequence, revealing a previously unknown lithic industry that underwent only minor changes over millennia.". That is, a technology that produced stone tools in the same manner over thousands of years and in a way that is different from other stone making tools!

People have been living here since before the Last Glacial Maximum (LGM) which took place between 19 and 26,000 years ago. This is long before the purporte "Beringian" standstill, (theory which assumes that Asians on their way to America stood still in Beringia because the LGM didn't let them into America).

The stones! the authors state: "The flaked artefacts reflect a technological tradition that was previously unknown, and remains mostly unchanged over the sequence." and they are quite unique: "...However, the majority of these tools are unifacial with marginal retouch... Apart from incipient preforms, finished bifacial artefacts are scarce; their existence is inferred from the abundance of tertiary thinning flakes. Notches and stems are almost completely absent. The bases are rounded or convergent, and are rarely thinned... Overall, the assemblage represents a lithic industry with no evident similarities to any of the other cultural complexes of the Pleistocene or Early Holocene epochs known in the Americas".

The authors conclude: "The occupants of the cave were seemingly adapted to altitudes and mountain landscapes, showing a behavioural pattern that—to our knowledge—was previously unknown in the archaeological record of the Americas. Their lithic industry has no parallel in the continent and its qualitative traits suggest a mature technology, possibly brought in from elsewhere before the LGM."

Of course the unusual stone tools and the lack of bones, ashes or hearths which would indicate actual human presence has been used by some skeptics to doubt the validity of this find. I quote some of them from this article in National Geographic below:

Loren Davis,Oregon State archaeologist: "The thing to remember is that humans don’t have a monopoly on the physics required to break rocks" (implying a natural origin for the unusual stone tools.
Tom Dillehay -discoverer of the Monteverde Site in Chile- "It's very curious that the assemblage is so different from anything anyone has known before. How is it possible that it’s not related to anything previously found? Well, it’s possible."

These are some of the tools (from the article):

They look man-made to me. And the tools found inside the cave were from stones of a green or black color (90% of the total) wich is interpreted as an act of human choice. Furthermore these stones are found close to the cave but not in it. The cave's rocks are grey so there is no doubt that they didn't fall from the cave's walls or roof.

To my inexperienced and non-academic eyes they look rather coarse and similar to Mousterian tools made by Neanderthals.

There is much to learn yet! But if humans were using these caves 35 Ky ago, then they must have arrived even earlier. In a Spanish language article one of the paper's authors -Ardelean- tells us that they found the cave following the indications given to them by a local farmer. That it took him a lot of work and effort to secure funding to excavate the cave; that there are few discoveries like this due to lack of funding and that the scarce funding goes into the "pyramids" (Mayan and Aztec ones) because they can be exploited as tourist attractions.

Ardelean added that "humans came to the caves now and then, they didn't live there, instead it was a winter shelter, probably part of a migration route".

Let's look forward to more discoveries like this one.

Wednesday, July 22, 2020

Nature article supports arrival of first Americans as far back as 57 Ky ago

An article published in Nature today (The timing and effect of the earliest human arrivals in North America Becerra-Valdivia, L., Higham, T. Nature (2020). https://doi.org/10.1038/s41586-020-2491-6 ) finds that:

"The data obtained show that humans were probably present before, during and immediately after the Last Glacial Maximum (about 26.5–19 thousand years ago)2,3 but that more widespread occupation began during a period of abrupt warming, Greenland Interstadial 1 (about 14.7–12.9 thousand years before 2000)4. We also identify the near-synchronous commencement of Beringian, Clovis and Western Stemmed cultural traditions, and an overlap of each with the last dates for the appearance of 18 now-extinct faunal genera. Our analysis suggests that the widespread expansion of humans through North America was a key factor in the extinction of large terrestrial mammals."

It is a first step in the right direction, and clearly states: "If transatlantic migration is set aside and an Asian origin assumed, the antiquity and distribution of the early sites suggest that the initial crossing of the 48th parallel north occurred either (i) during the later part of Marine Isotope Stage 3 (57–29 ka)36, when ice and sea level estimates37–39 indicate that land passage through Beringia was unlikely or interrupted, and an ice-free corridor between the Laurentide and Cordilleran Ice Sheets was probably present39 (with evidence of terrestrial landscapes occurring between 48 and 40 ka40) or (ii) during the LGM terminus, when the Bering land bridge was viable but the ice-free corridor was inaccessible41,42. Both possibilities sug-gest the earliest arrivals to North America had some degree of littoral adaptation."

The Clovis First theory has bean dealt a great blow! The authors write: "the previously accepted model (termed ‘Clovis-first’)—suggesting that the first inhabitants of the Americas were linked with the Clovis tradition, a complex marked by distinctive fluted lithic points1—has been effectively refuted".

It mentions several Pre-Clovis sites: "pre-Clovis sites show the earli-est evidence for cultural occupation in stratigraphic component C of Chiquihuite Cave (Mexico) at 33,150–31,405 cal., before the Last Glacial Maximum (LGM) (from 26.5 to 20–19 ka2,3). Several sites appear to be occupied later, during or immediately after the LGM. These include Gault (26,435–17,385cal.), Meadowcroft Rockshelter (24,335–18,620cal.) and Cactus Hill (20,585–18,970cal.) (Fig.2a). In eastern Beringia, Bluefish Caves is represented by a single date obtained on a humanly modified bone sample (24,035–23,310cal.) dating squarely to the LGM..

It is encouraging, and should undo the dark work of William Henry Holmes of the Smithsonian Institution, Thomas Chamberlin of the United States Geological Survey and Ales Hrdlicka (of the Smithsonian) who refused to accept that humans had reached America before the end of the last Ice Age. They imposed their ideas and only accepted an earlier (but not too early) date when the Folsom points were found in 1927 followed by the Clovis ones in the 1930s. They were irrefutable confirmation of ancient humans in the Americas during the Pleistocene.

But pushing the dates beyond 12-13,000 years has proven difficult. Let's hope this article marks a new trend in the field.

Saturday, July 18, 2020

The Neanderthal from Chagyrskaya

A recent paper (A high-coverage Neandertal genome from Chagyrskaya Cave by Fabrizio Mafessoni et al. Proceedings of the National Academy of Sciences Jun 2020, 117 (26) 15132-15136; DOI: 10.1073/pnas.2004944117) reported the sequencing of a third Neandertal genome. It complements the other two, one from the Denisova Cave in the Altai Mountains, the other from the Vindija cave in Croatia.

The Neandertal from Chagyrskaya -a site which is roughly 66 miles (106 km) from Denisova is significant because Chagyrskaya specimen lived around 80,000 years ago, the Denisovan Neandertal lived roughly 110,000 years ago and Vindija's specimen has been dated to around 50,000 years ago.

But despite the geographical closeness between Chagyrskaya and Denisova, Chagyrskaya is closer to the European Neanderthals: it "...shares more derived alleles with Vindija 33.19 and other later Neandertals in the Caucasus and in Europe than with the older Denisova 5 Neandertal from the Altai".

The authors also found that " that Vindija 33.19 is more closely related than Chagyrskaya 8 to Neandertal populations that contributed the majority of the DNA to present-day populations." that is, modern humans are closr to Vindija Neandertals than to the Chagyrskaya one.

Finally, they conclude that "Chagyrskaya 8 is thus related to Neandertal populations that moved east sometime between 120 and 80 kya. Interestingly, the artifacts found in Chagyrskaya Cave show similarities to artifact assemblages in central and eastern Europe, suggesting that Neandertal populations coming from western Eurasia to Siberia may have brought their material culture with them. Some of these incoming Neandertals encountered local Denisovan populations, as shown by Denisova 11, who had a Denisovan father and a Neandertal mother related to the population in which Chagyrskaya 8 lived."

Friday, July 17, 2020

Amerindians navigated to Polynesia before the Polynesians arrived there

An article in Nature (Native American gene flow into Polynesia predating Easter Island settlement, Ioannidis, A.G., Blanco-Portillo, J., Sandoval, K. et al. Nature (2020). https://doi.org/10.1038/s41586-020-2487-2) finds evidence that there is Amerindian admixture in Polynesian people due to an early "one-time-only" event that took place around 1150-1230 AD in eastern Polynesia.

The Amerindians didn't sail to Easter Island (Rapa Nui) which is the point where America and Polynesia are closest. Instead they moved across the equatorial region -like Thor Heyerdahl had suggested in the 1940s- and reached the Marquesas islands, which at that time were uninhabited.

Then came the island-hopping Polynesians from the west and they met there, admixed and then spread across the Pacific.

The authors find similarities between the DNA sampled in Polynesia with the DNA of Colombian and Ecuadorian Native Americans.

A plausible alternative is that the Amerindians never set sail across the ocean. Instead the Polynesians kept on sailing eastwards and reached America, here they fraternized with the locals and returned with Amerindian DNA back home.

The Polynesia to America route has been proposed before (Diffusionism Reconsidered: Linguistic and Archaeological Evidence for Prehistoric Polynesian Contact with Southern California Terry L. Jones and Kathryn A. Klar American Antiquity, Vol. 70, No. 3 (Jul., 2005), pp. 457-484 DOI: 10.2307/40035309). And I have posted about Polynesian DNA in South America (here) regarding the Botocudo people and a possible route for peopling America via the Antarctic (read more ), but for pre-Polynesian people -I was thinking about Aboriginals from Australia or even pre-sapiens hominins (here), not Polynesians who are the latecomers to the region.

Alternate Hypothesis

Perhaps the Amerindian signal has another origin. Let's take a look at the map in Nature's paper:

See large size map

The "Polynesians" supposedly have a strong imprint of Amerindian -green- DNA. And the Chilean Mapuche people (brown) are found in large amounts in Easter Island, which is coherent with the Spanish from Chile visiting the islands with native servants-laborer, and from there back migrated into western Polynesia in historic times. They also occupy the Chilean-Argentine area of South America. The ancestral Kaweskar people who were "canoe people" have a high prevalence of the "green" signal. They were the first to reach southern South America.

The strong Mesoamerican signal may (green) may indicate that these people (Mixe, Zapotec, Maya, Northern South American Amerindians and the ancestral Kaweskar) came from Polynesia -from Asia via Polynesia. They also settled there in their migration from Asia to America. Later came the (pale blue) wave of Polynesians and replaced them.

Sunday, April 5, 2020

Homo antecessor and its relationship with Neandethals, Denisovans and Humans

Covid-19 is disrupting the lives across the world with its path of sickness and death spreading globally. But science continues. Today I post about an article published in Nature this week: Welker, F., Ramos-Madrigal, J., Gutenbrunner, P. et al. The dental proteome of Homo antecessor Nature (2020). https://doi.org/10.1038/s41586-020-2153-8.

The authors studied proteins from the teeth enamel -which degrade slower than DNA. These proteins came from a specimen of Homo antecessor, a hominin that lived in Spain (Atapuerca) 800 kya, and Dmanisi Homo erectus (1.77 My old). They compared them to those of Modern Humans, Neanderthals and Denisovans.

Their abstract highlights the following (quote):

"H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans."
"The modern-like face of H. antecessor—that is, similar to that of modern humans—may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form."

The trees built by the authors show that both Dmanisi and Antecessor are part of our tree, but both lie on branches that do not lead to us. We branched from them. More evidence is needed to find these homins who cover the gap between us and them.

Note that the protein from the Dmanisi erectus was too damaged to provide useful information.

Keep safe, wash your hands, wear a mask and practice social distancing.

Written in an Argentina in isolation and lockdown.

Monday, February 24, 2020

Neandersovans mixed with Superarchaics as they entered Eurasia 700 kya

Six years ago I wrote a post (Denisovans interbred with Homo erectus) based on an article that suggested that Denisovans had admixed with a "ghost" population that had split from the line that links us and Denisovans, around 1 Millioni years ago. In my post I guessed that this ancestor was no other than Homo erectus.

A very recent paper (see full text: Neanderthal-Denisovan ancestors interbred with a distantly related hominin, Alan R. Rogers, Nathan S. Harris and Alan A. Achenbac. Science Advances 20 Feb 2020:Vol. 6, no. 8, eaay5483 DOI: 10.1126/sciadv.aay5483) came to that same conclusion after some interesting genetic analysis.

The Abstract of this paper says:

"... We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors—members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans."

The paper looks into the "large-brained hominins" living in Europe, that made Acheulean stone tools some 600,000 year. It calls them Neanderthal ancestors. They come from the "neandersovan" group, from which Neanderthals and Denisovans descend. And which split from our modern human lineage around 750 kya. The neandersovans left Africa and walked into Eurasia, which was not an empty territory. It had already been colonized some 1.85 Million years ago by other hominins, the "superarchaic" population.

Did they mix?

Yes, they did.

The authors consider that "If superarchaics separated from an African population, then this separation must have preceded the arrival of superarchaics in Eurasia. Nonetheless, our 1.8 to 2.2 Ma interval includes the 1.85 Ma date of the earliest Eurasian archaeological remains at Dmanisi. Thus, superarchaics may descend from the earliest human dispersal into Eurasia, as represented by the Dmanisi fossils. On the other hand, some authors prefer a higher mutation rate of 0.5 × 10−9 per year. Under this clock, the lower end of our confidence interval would be 1.6 Ma ago. Thus, our results are also consistent with the view that superarchaics entered Eurasia after the earliest remains at Dmanisi.".

So depending on the mutation rate adopted, they could have mixed with the descendants of the Dmanisi people from Georgia or from a later group. Dmanisi may be Homo habilis or Homo erectus.

The paper proposes that there were "... only three expansions of humans from Africa into Eurasia: an expansion of early Homo at about 1.9 Ma ago, an expansion of neandersovans at about 700 ka ago, and an expansion of modern humans at about 50 ka ago.". This first expansion led to the superarchaic population in Eurasia that mixed with the second wave of "neandersovans" 700 kya.

The scenario painted in the paper is the following: "Our results indicate that neandersovans interbred with superarchaics early in the middle Pleistocene, shortly after expanding into Eurasia. This is the earliest known admixture between hominin populations. Furthermore, the two populations involved were more distantly related than any pair of human populations previously known to interbreed. According to our estimates, neandersovans and superarchaics had been separate for about 1.2 Ma. Later, when superarchaics exchanged genes with Denisovans, the two populations had been separate even longer. By comparison, the Neanderthals and Denisovans who interbred with modern humans had been separate less than 0.7 Ma.".

Monday, February 3, 2020

The complex Human tree in Africa...

A new paper published in Nature (Ancient West African foragers in the context of African population history, Mark Lipson, Isabelle Ribot, David Reich. Nature 577, 665–670 (2020). https://doi.org/10.1038/s41586-020-1929-1) tells us about the admixture going on in Africa some thousands of years ago:

The paper's highlights are:

They sequenced the DNA of four children from Shum Laka in Cameroon buried on two separate occasions (two of the children were buried 8,000 years ago, the other two, 3,000 years ago).
One of them carried the oldest and most divergent Y chromosome haplogroup: A00
Their model implies that these children belong to the fourth group that originated modern human lineages. There were three more groups: (i) from which modern Khoisan people descend from. (ii) Ancestral group to the East Africans. (iii) An exinct "ghost" population. These groups are some 250 ky old.

Science tells us more about the extinct group (iii): "Another two-thirds of children’s DNA came from an ancient "basal" source in West Africa, including some from a "long lost ghost population of modern humans that we didn’t know about before" says population geneticist David Reich of Harvard University, leader of the study."

And even more interesting is that "...the Shum Laka individuals are most related to present day rainforest hunter-gatherers [pygmies] and not ancestors of Bantu-speakers is surprising given that Shum Laka was long considered by archeologist[s] as the site where Bantu-speaker culture [was] developing in situ," (from LiveScience)

These four children are therefore not related to the modern Africans living in Cameroon or to the Bantu speakers who spread out across Africa. Instead they are closer to the pygmies of Central Africa!

Neanderthal genes in Africans: a confirmed fact

Last October I posted about a paper that disclosed that Africans had a higher Neanderthal signature in their mtDNA than Asians or Europeans.

African lack of Neanderthal DNA (and mtDNA) is used as proof of the Out of Africa (OOA) event, because it is said that Neanderthals and Homo sapiens admixed outside of Africa after H. sapiens migrated from Africa on their OOA journey.

A recent paper cast a shadow of doubt on this assumption: they have found signals of Neanderthal DNA in Africans!

The paper is: Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals by Lu Chen, Aaron B. Wolf, Wenqing Fu, Liming Li, and Joshua M. Akey. Chen et al., 2020, Cell 180, 1–11 February 20, 2020 https://doi.org/10.1016/j.cell.2020.01.012.

It summarizes their research as follows:

"Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date"

The paper finds that some of the ancestors of modern Europeans back migrated into Africa after they had split from those who would later become East Asians.

They found 13 African-specific high-frequency Neanderthal haplotypes which are unique to Africans, and only found in Africa, and another 31< haplotypes shared with Europeans. Specific African genes means that selection preserved them because they gave those carrying them some immune benefits and also protection against UV radiation in sunlight.

So now we know that ALL humans have Neanderthal genes in their genome, including Africans.

This gene flow, which had not been recognized until now also caused biased estimations of Neanderthal admixture in Asians and Europeans: East Asians seemed to have 20% more Neanderthal DNA than Europeans, which was odd, considering that Neanderthals lived in western Eurasia so admixture there would have been higher than in the Far East.

But now it seems that roughly 0.3 to 0.5 % of African genome was inherited from Neanderthals (vs. 1.8% in Non-Africans).

So factoring in this African Neanderthal content, the East Asians ended up with only 8% more Neanderthal genes than Europeans.

The study found "[in] African populations, we identified approximately 17 Mb of putative Neanderthal sequence per individual"

Compare thiese 17Mb with what they found in Europeans and Asians:

"we found similar levels of Neanderthal ancestry in Europeans (51 Mb/individual), East Asians (55 Mb/individual), and South Asians (55 Mb/individual)"

So Africans have roughly one third of the Neanderthal admixture that non-Africans have! See the image below which shows exactly this (non-Africans in Blue, Africans in brown):

Neanderthal genetic admixture in humans. From Fig. 2 in Chen et al.

Finally, around 94 percent of Neandertal DNA sequences found in Modern Africans is also shared with Non-Africans.

The paper explains the Neanderthal admixture into Africa as follows: "In summary, these data indicate that both pre-OOA human-to-Neanderthal gene flow and elevated historic backmigration contribute to the signal of Neanderthal ancestry detected in Africans.".

The first wave of humans to leave Africa between 250 and 150 kya, mixed with Neanderthals in Eurasia and passed on to them some archaic human genes. These were lost as this pre-OOA wave became extinct. The Neanderthals then mixed with the OOA wave and part of these admixed modern Humans returned to Africa bringing the genes with them.

Perhaps further studies -Science news reports an unpublished study that ratifies Chen et al. findings: "as-yet-unpublished work by Sarah Tishkoff, an evolutionary geneticist at the University of Pennsylvania. She told Science she has also found higher-than-expected levels of apparent Neanderthal DNA in Africans."

I have written many posts about "into Africa events", but this one is the first paper to conclusively prove the presence of Neanderthal genes in modern Africans.

This will open the gates to more scrutiny on the origin of the higher "African" diversity when compared to the rest of humankind. This diversity is surely due to admixture with archaic populations and not only to bottlenecks caused by an OOA migration.

Saturday, January 4, 2020

Mammoth killed by humans in Beringia 21,000 years ago

A very short post to mention an article (Arctic island woolly mammoth shows strongest evidence yet of human slaughter and butchering. Siberian Times, 03 January 2020) which states that the remains of a woolly mammoth were found on Kotelny island and radiocarbon dated to approx. 21,000 years ago.

Kotelny island was part of the land bridge that linked Asia and America during that time. The animal was "killed and butchered" by "ancient people" according to Dr Albert Protopopov.

map showing location of Kotelny Island.

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