Deepest Neandertal mtDNA split

The authors interpret the new result from HST as placing a lower boundary on an introgression from Africans to Neandertals at more than 290kya, which explains why Africans are genomically closer to Neandertals than to Denisovans.

Of course, when one looks at the mitochondrial phylogeny, it has the form:

(Denisovans, (Neandertals, Modern Humans))

Within the Modern Humans, Eurasians are a branch of a tree which is mostly African. This has been interpreted for decades as evidence for the Out of Africa hypothesis for the origin of Modern Humans. But, within the phylogeny as a whole, Modern Humans are a branch of the Eurasian tree. This has not (why?) in general been interpreted as evidence for Out of Eurasia for the common ancestor of Modern Humans and Neandertals.

It seems to me that this hypothesis, that Modern Humans and Neandertals stem from a non-African ancestor (a non-African population of H. heidelbergensis, for example), has much to recommend it.

Eurasia has twice the size of Africa and has been home to hominins for ~1.8 million years. It was inhabited by diverse hominins, and thanks to blind luck we discovered that as late as a few tens of thousands years ago, it also sported two of the populations that split off before anyone else: first H. floresiensis, and second Denisovans.

While a North African source of modern humans is plausible, the data seems to favor a Eurasian origin of the (Modern Human, Neandertal) ancestor.

Nature Communications 8, Article number: 16046 (2017) doi:10.1038/ncomms16046

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

Cosimo Posth, Christoph Wißing, Keiko Kitagawa, Luca Pagani, Laura van Holstein, Fernando Racimo, Kurt Wehrberger, Nicholas J. Conard, Claus Joachim Kind, Hervé Bocherens & Johannes Krause

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.

Link

700 thousand year old ancestors of H. floresiensis

Nature 534, 245–248 (09 June 2016) doi:10.1038/nature17999

Homo floresiensis-like fossils from the early Middle Pleistocene of Flores

Gerrit D. van den Bergh, Yousuke Kaifu, Iwan Kurniawan, Reiko T. Kono, Adam Brumm, Erick Setiyabudi, Fachroel Aziz & Michael J. Morwood

The evolutionary origin of Homo floresiensis, a diminutive hominin species previously known only by skeletal remains from Liang Bua in western Flores, Indonesia, has been intensively debated. It is a matter of controversy whether this primitive form, dated to the Late Pleistocene, evolved from early Asian Homo erectus and represents a unique and striking case of evolutionary reversal in hominin body and brain size within an insular environment1, 2, 3, 4. The alternative hypothesis is that H. floresiensis derived from an older, smaller-brained member of our genus, such as Homo habilis, or perhaps even late Australopithecus, signalling a hitherto undocumented dispersal of hominins from Africa into eastern Asia by two million years ago (2 Ma)5, 6. Here we describe hominin fossils excavated in 2014 from an early Middle Pleistocene site (Mata Menge) in the So’a Basin of central Flores. These specimens comprise a mandible fragment and six isolated teeth belonging to at least three small-jawed and small-toothed individuals. Dating to ~0.7 Ma, these fossils now constitute the oldest hominin remains from Flores7. The Mata Menge mandible and teeth are similar in dimensions and morphological characteristics to those of H. floresiensis from Liang Bua. The exception is the mandibular first molar, which retains a more primitive condition. Notably, the Mata Menge mandible and molar are even smaller in size than those of the two existing H. floresiensis individuals from Liang Bua. The Mata Menge fossils are derived compared with Australopithecus and H. habilis, and so tend to support the view that H. floresiensis is a dwarfed descendent of early Asian H. erectus. Our findings suggest that hominins on Flores had acquired extremely small body size and other morphological traits specific to H. floresiensis at an unexpectedly early time.

Link

Nature 534, 249–253 (09 June 2016) doi:10.1038/nature17663

Age and context of the oldest known hominin fossils from Flores

Adam Brumm, Gerrit D. van den Bergh, Michael Storey, Iwan Kurniawan, Brent V. Alloway, Ruly Setiawan, Erick Setiyabudi, Rainer Grün, Mark W. Moore, Dida Yurnaldi, Mika R. Puspaningrum, Unggul P. Wibowo, Halmi Insani, Indra Sutisna, John A. Westgate, Nick J. G. Pearce, Mathieu Duval, Hanneke J. M. Meijer, Fachroel Aziz, Thomas Sutikna, Sander van der Kaars, Stephanie Flude & Michael J. Morwood

Recent excavations at the early Middle Pleistocene site of Mata Menge in the So’a Basin of central Flores, Indonesia, have yielded hominin fossils1 attributed to a population ancestral to Late Pleistocene Homo floresiensis2. Here we describe the age and context of the Mata Menge hominin specimens and associated archaeological findings. The fluvial sandstone layer from which the in situ fossils were excavated in 2014 was deposited in a small valley stream around 700 thousand years ago, as indicated by 40Ar/39Ar and fission track dates on stratigraphically bracketing volcanic ash and pyroclastic density current deposits, in combination with coupled uranium-series and electron spin resonance dating of fossil teeth. Palaeoenvironmental data indicate a relatively dry climate in the So’a Basin during the early Middle Pleistocene, while various lines of evidence suggest the hominins inhabited a savannah-like open grassland habitat with a wetland component. The hominin fossils occur alongside the remains of an insular fauna and a simple stone technology that is markedly similar to that associated with Late Pleistocene H. floresiensis.

Link

Middle (not Upper) Paleolithic hobbits

Nature (2016) doi:10.1038/nature17179

Revised stratigraphy and chronology for Homo floresiensis at Liang Bua in Indonesia

Thomas Sutikna, Matthew W. Tocheri, Michael J. Morwood, E. Wahyu Saptomo, Jatmiko, Rokus Due Awe, Sri Wasisto, Kira E. Westaway, Maxime Aubert, Bo Li, Jian-xin Zhao, Michael Storey, Brent V. Alloway, Mike W. Morley, Hanneke J. M. Meijer, Gerrit D. van den Bergh, Rainer Grün, Anthony Dosseto, Adam Brumm, William L. Jungers & Richard G. Roberts

Homo floresiensis, a primitive hominin species discovered in Late Pleistocene sediments at Liang Bua (Flores, Indonesia)1, 2, 3, has generated wide interest and scientific debate. A major reason this taxon is controversial is because the H. floresiensis-bearing deposits, which include associated stone artefacts2, 3, 4 and remains of other extinct endemic fauna5, 6, were dated to between about 95 and 12 thousand calendar years (kyr) ago2, 3, 7. These ages suggested that H. floresiensis survived until long after modern humans reached Australia by ~50 kyr ago8, 9, 10. Here we report new stratigraphic and chronological evidence from Liang Bua that does not support the ages inferred previously for the H. floresiensis holotype (LB1), ~18 thousand calibrated radiocarbon years before present (kyr cal. BP), or the time of last appearance of this species (about 17 or 13–11 kyr cal. BP)1, 2, 3, 7, 11. Instead, the skeletal remains of H. floresiensis and the deposits containing them are dated to between about 100 and 60 kyr ago, whereas stone artefacts attributable to this species range from about 190 to 50 kyr in age. Whether H. floresiensis survived after 50 kyr ago—potentially encountering modern humans on Flores or other hominins dispersing through southeast Asia, such as Denisovans12, 13—is an open question.

Link

Did Men cause the demise of the Hobbits?

An interesting tidbit from an interview with Chris Stringer:

There was also a population of a very small human-like species on the island of Flores in Indonesia—often called "hobbits." It had been thought they were around until about 17,000 years ago, but unpublished evidence suggests they could have disappeared earlier, in which case the spread of modern humans might correlate with their demise.

and:

My model is that modern humans came out of Africa 60,000 years ago and moved very quickly into the territory of the Neanderthals, later into the territory of the Denisovans, and soon after that into the territory of the "hobbits." Within 20,000 years, as far as we can tell, those other populations have gone, all of them. 

Was Homo floresiensis a cretin?

From the paper:

We are therefore disturbed that Brown (2012), though selecting those features that imply to him that LB1 could not be a cretin, does not also cite the many features in those same publications that imply cretinism, nor does he cite the many more features, both observational and quantitative implying cretinism, in Oxnard (2008), Oxnard et al. (2011), and Dennison et al. (2012). What is sorely needed is an independent review of, and free access to, the Liang Bua material.

HOMO - Journal of Comparative Human Biology
Volume 63, Issue 6, December 2012, Pages 407–412

More on the Liang Bua finds and modern human cretins

Charles Oxnard et al.

Brown (2012: LB1 and LB6 Homo floresiensis are not modern human (Homo sapiens) cretins, Journal of Human Evolution) makes errors of fact, omission and interpretation. Brown's comments refer, among others, to (1) delayed growth and development indicated by unfused epiphyses, (2) postcranial limb proportions: limbs to trunk, between limbs, and within limbs, (3) postcranial bone torsions and angles, (4) postcranial robusticity, real and apparent, (5) skull features, and (6) cretinism on Flores. In each of these areas, much information about cretins is incorrect and much information (Oxnard et al., 2010) comparing the Liang Bua remains with cretins is ignored.

Link

DNA half-life + Old Hobbits

New Scientist reports on a new paper that attempts to quantify the "half-life" of DNA. This bit caught my eye:

Unfortunately, Bunce thinks the new calculations will be difficult to apply to specific sites. "A host of other factors come into play," he says, including the season the organism died. In fact, although the moa bones in the analysis had been buried in a similar environment, the age of the specimens could account for only about 40 per cent of the variation in DNA preservation – in other words, the half-life signal is noisy. 

Alan Cooper, director of the Australian Centre for Ancient DNA at the University of Adelaide, South Australia, agrees. "The rotting process after death is very seasonal and context dependent, and has a major impact on DNA survival." 

Cooper has attempted to extract DNA from Homo floresiensis remains, but is beginning to think that none will ever be found. He says that recent unpublished dating estimates indicate that "the hobbit material may be considerably older than currently suggested".

The paper probably has implications for many areas of biology, but the recent sequencing of the Denisova hominin at high coverage, leaves me hopeful that we will have some type of ancient DNA evidence for at least the last 100 thousand years, quite a lot of it for the time since the inception of the Upper Paleolithic, and nearly everything for the time since the beginning of the Neolithic.

Proc. R. Soc. B doi: 10.1098/rspb.2012.1745

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

Morten E. Allentoft et al.

Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 ? 10–6 per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R2 = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.

Link

ESHE 2012 abstracts

Some abstracts of interest from the European Society for the study of Human Evolution 2012 meeting (pdf). To avoid making this too long, I will just post the titles and the most relevant quotes. You can read the abstracts in the linked pdf for authors names and more information.

Neandertal and Denisovan Genomes from the Altai 

Susanna Sawyer  et al.

In 2010 a draft genome sequence was determined from a small finger bone found in Denisova Cave in southern Siberia. Its analysis revealed that it derives from an individual who belonged to a population related to, but distinct from, Neandertals. A molar has also been described from Denisova Cave and has shown to carry an mtDNA genome closely related to that of the finger bone.  We have recently determined the DNA sequence of the Denisova genome to a quality similar to present-day human genomes. We have also retrieved a complete mitochondrial genome and nuclear DNA sequences from an additional molar found in Denisova Cave. Furthermore, we have determined a high-quality nuclear genome from a pedal phalanx found in Denisova Cave in 2010. We show that the pedal phalanx derived from a Neandertal and thus that Neandertals as well as Denisovans have been present in the cave. We will discuss the genetic history of Denisovans as well as Neandertals in light of these new genome sequences. 

The discovery of a Neandertal genome from Denisova cave is certainly interesting. I have previously commented that:

If Vindija and Denisova, two caves less than 5,000km apart were home to people more divergent from each other than any two humans are today, it's strange to think that only "modern humans" inhabited Africa at the same time.

Now, it appears that Neandertals and Denisovans were present (when?) not only 5Mm apart, but literally on the same spot. Much later, during the Neolithic we see very differentiated humans co-existing in Europe. And, we get archaic hominins in Africa long after the appearance of anatomically modern humans there. I think the evidence is looking good for my hypothesis that regional human populations have recently gotten more similar over time through extensive admixture between divergent hominin groups, rather than that they became more dissimilar over time  through tree-like divergence.

On the same topic, here is more evidence for Neandertal presence in the Altai:

A Neanderthal mandible fragment from Chagyrskaya Cave (Altai Mountains, Russian Federation)

Both the mandible and the dentition preserve numerous derived Neanderthal traits: among else a posteriorly placed mandibular foramen, an oblique mylohyoid line, an asymmetrical P4 and continuous mid-trigonid crests on the M1 and M2. ... Ongoing ancient DNA analyses of the hominin remains from Chagyrskaya cave and absolute dates for the site will hopefully help to clarify the origin of the Altai Neanderthals, and their relationship with the Denisovans.

An hypothesis for the phylogenetic position of Homo floresiensis

Our cladistic analysis places H. floresiensis unequivocally as part of a clade with H. habilis

Who are you calling ”modern”? An assessment of the dental morphology and metrics of Homo sapiens

Although dental reduction has long been cited as a derived feature of H. sapiens, our data indicate this claim may be no longer tenable ... the single metrical assessment that groups all H. sapiens (early, Upper Paleolithic and recent) apart from other taxa is the ratio between mandibular:maxillary crown areas.  the results of our study are important for assessing recent claims of great antiquity for H. sapiens outside of Africa

Neanderthal in Malthusian demographic trap

It can be hypothesized that the demography of the Neanderthal metapopulation, living under conditions where extreme environmental instability with short periods was the norm, was primarily stagnant,

with frequent bottlenecks and episodes of decline.

 A New Framework for the Upper Paleolithic of Eastern Europe

The results of field and laboratory research during the past decade require a new classificatory framework for the Upper Paleolithic in Eastern Europe. It is now apparent that people making artifacts assigned to the Ahmarian industry occupied both the southern and northern slopes of the Caucasus Mountains (i.e., Ortvale Klde, Layer 4d; Mezmaiskaya Cave, Layer 1C). Their sites probably indicate a separate movement of anatomically modern humans (AMH) from the Near East directly into Eastern Europe, establishing an independent line of development during the earlier Upper Paleolithic that parallels the Proto-Aurignacian and Aurignacian sequence in Western and Central Europe. this East European industry is most fully represented at the Kostenki-Borshchevo sites on the Don River before 40,000 cal BP (e.g., Kostenki 14, Layer IVb). It is followed by a closely related industry, also characterized by bladelet production, that is dated to the interval between 40,000 and 30,000 cal BP in Crimea and the East European Plain. The proposed new framework reflects recognition of these distinctive East European entities and of two environmental events that had significant impacts on human settlement in Eastern Europe: (1) the Campanian Ignimbrite (CI) volcanic eruption (40,000 cal BP); and (2) the Last Glacial Maximum (LGM) ( 25,000 cal BP). It has been suggested that the early Upper Paleolithic (EUP) industry present in Eastern Europe before 40,000 cal BP should be labeled an eastern variant of the contemporaneous Proto-Aurignacian of Mediterranean Europe. However, given the separate movement of people from the Near East via the Caucasus Mountains, and independent development of the East European EUP, this industry is more appropriately termed “Proto-Gravettian.” The younger bladelet industry, which includes assemblages at Buran-Kaya III (Layer 6-1), Mira (Layer II/2), Kostenki 8 (Layer II), and probably Shlyakh (Layers 4C, 6), may be termed “Early Gravettian” to distinguish it from the classic Gravettian industry that dates to less than 30,000 cal BP (e.g., Avdeevo, Zaraisk).The upper temporal boundary of the Proto-Gravettian corresponds to the CI eruption (40,000 cal BP), while the classic Gravettian of the East European Plain appears to have been effectively terminated by the LGM ( 25,000 cal BP). Several sites that date to the 40,000–30,000 cal BP interval (e.g., Kostenki 1, Layer III) contain elements that suggest a connection with the Aurignacian technocomplex of Western-Central Europe. These assemblages may be placed into the category of “Eastern Aurignacian,” which reflects differences in content with the West and Central European sites. The apparent spread of this industry into Eastern Europe from Central Europe may be related to the impact of the CI eruption on portions of the East European Plain. 

 Conflicting dates for the Late Aterian

First at the huge Ifri n’Ammar sites, TL dates have indicated 80,000 years for the Late Middle Palaeolithic/Aterian levels. Our new C14 dates yield 35,000 BP for exactly the same levels. At the “grotte des Contrebandiers”, formerly dated at 28,000 BP by Debenath and his team, is now dated at 100,000 years by new TL dates. As starting points, this kind of methodological contradiction should be confronted, understood and resolved.

 The Rio Secco Cave in the North Adriatic Region, Italy. A new context for investigating the Neanderthal demise and the settllement of Anatomically Modern Humans

A sequence of several thin layers dated to 46.0–42.1ky Cal BP represents the final Mousterian.

The Dhofar Nubian Tradition: an enduring Middle Stone Age technocomplex in southern Arabia

Between 2010 and 2012, the Dhofar Archaeological Project has located and mapped 260 Nubian Complex occurrences across the Nejd Plateau of southern Oman. Diagnostic Nubian artifacts werefound cemented in fluvial sediments at the site of Aybut Al Auwal in Dhofar, with two OSL dates around 106 ka BP; hence, roughly contemporaneous with the African Nubian Complex (Rose et al. 2011). Many of these lithic assemblages, such as that from Aybut al Auwal, are technologically homologous to the Late Nubian Industry found in northeast Africa, sensu stricto, while others may represent local facies of the greater “Afro-Arabian Nubian Technocomplex.” This presentation describes the various reduction strategies encountered at a sample of Nubian Complex sites from Oman, explores inter-assemblage variability, and begins to articulate technological units within the “Dhofar Nubian Tradition.” To achieve this aim, we have developed an analytical scheme with which to describe technological variability among Nubian Levallois reduction strategies in both Africa and Arabia. Our analysis indicates at least two distinct Nubian industries. The first, which we refer to as the “Classic Dhofar Nubian,” is virtually identical to Late Nubian Industry from the Lower Nile Valley and Red Sea Hills in Egypt. Thee subsequent group of assemblages in Dhofar, called the “Mudayyan,” exhibits a technological shift toward diminutive Nubian Levallois cores and that, recurrent bidirectional cores with opposed, faceted striking platforms. We interpret this evidence to indicate an enduring, local Nubian tradition in Dhofar that is ultimately rooted in the African Nubian Complex. 

From Late Mousterian to Evolved Aurignacian: New evidence for the Middle-to-Upper Paleolithic transition in Mediterranean Spain

Combined, the evidence from CA and FDM indicates that, in chronostratigraphic terms, the Middle-to-Upper Paleolithic transition in Murcia consists of the replacement of a Late Mousterian by an Evolved Aurignacian and occurred some time during the 38th millennium cal BP

Homo floresiensis: dramatically dwarfed Homo erectus descendant

Journal of Human Evolution doi:10.1016/j.jhevol.2011.08.008

Craniofacial morphology of Homo floresiensis: Description, taxonomic affinities, and evolutionary implication

Yousuke Kaifu et al.

This paper describes in detail the external morphology of LB1/1, the nearly complete and only known cranium of Homo floresiensis. Comparisons were made with a large sample of early groups of the genus Homo to assess primitive, derived, and unique craniofacial traits of LB1 and discuss its evolution. Principal cranial shape differences between H. floresiensis and Homo sapiens are also explored metrically.

The LB1 specimen exhibits a marked reductive trend in its facial skeleton, which is comparable to the H. sapiens condition and is probably associated with reduced masticatory stresses. However, LB1 is craniometrically different from H. sapiens showing an extremely small overall cranial size, and the combination of a primitive low and anteriorly narrow vault shape, a relatively prognathic face, a rounded oval foramen that is greatly separated anteriorly from the carotid canal/jugular foramen, and a unique, tall orbital shape. Whereas the neurocranium of LB1 is as small as that of some Homo habilis specimens, it exhibits laterally expanded parietals, a weak suprameatal crest, a moderately flexed occipital, a marked facial reduction, and many other derived features that characterize post-habilis Homo. Other craniofacial characteristics of LB1 include, for example, a relatively narrow frontal squama with flattened right and left sides, a marked frontal keel, posteriorly divergent temporal lines, a posteriorly flexed anteromedial corner of the mandibular fossa, a bulbous lateral end of the supraorbital torus, and a forward protruding maxillary body with a distinct infraorbital sulcus. LB1 is most similar to early Javanese Homo erectus from Sangiran and Trinil in these and other aspects. We conclude that the craniofacial morphology of LB1 is consistent with the hypothesis that H. floresiensis evolved from early Javanese H. erectus with dramatic island dwarfism. However, further field discoveries of early hominin skeletal remains from Flores and detailed analyses of the finds are needed to understand the evolutionary history of this endemic hominin species.

Link