Laura Longo

A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals

The melanocortin 1 receptor (MC1R) regulates pigmentation in humans and other vertebrates. Variants of MC1R with reduced function are associated with pale skin color and red hair in humans of primarily European origin. We amplified and sequenced a fragment of the MC1R gene (mc1r) from two Neanderthal remains. Both specimens have a mutation that was not found in ∼3700 modern humans analyzed. Functional analyses show that this variant reduces MC1R activity to a level that alters hair and/or skin pigmentation in humans. The impaired activity of this variant suggests that Neanderthals varied in pigmentation levels, potentially on the scale observed in modern humans. Our data suggest that inactive MC1R variants evolved independently in both modern humans and Neanderthals.

Thirty thousand-year-old evidence of plant food processing

European Paleolithic subsistence is assumed to have been largely based on animal protein and fat, whereas evidence for plant consumption is rare. We present evidence of starch grains from various wild plants on the surfaces of grinding tools at the sites of Bilancino II (Italy), Kostenki 16–Uglyanka (Russia), and Pavlov VI (Czech Republic). The samples originate from a variety of geographical and environmental contexts, ranging from northeastern Europe to the central Mediterranean, and dated to the Mid-Upper Paleolithic (Gravettian and Gorodtsovian). The three sites suggest that vegetal food processing, and possibly the production of flour, was a common practice, widespread across Europe from at least ~30,000 y ago. It is likely that high energy content plant foods were available and were used as components of the food economy of these mobile hunter–gatherers.

A highly divergent mtDNA sequence in a Neandertal individual from Italy

Neandertals are documented in Europe and Western Asia from about 230,000 to 29,000 years ago. Analyses of mitochondrial DNA (mtDNA) from Neandertal samples [1,2] and other analyses [3–5] appear incompatible with the hypothesis that Neandertals are direct ancestors of modern Europeans [6,7]. However, there are broad geographic gaps in the sampling of Neandertal DNA diversity. Here, we describe the sequence of the first mitochondrial hypervariable region (HVR1) in a new specimen from Monti Lessini (MLS) in Northern Italy.

Specific inactivation of two immunomodulatory SIGLEC genes during human evolution

Sialic acid-recognizing Ig-like lectins (Siglecs) are signaling receptors that modulate immune responses, and are targeted for interactions by certain pathogens. We describe two primate Siglecs that were rendered nonfunctional by single genetic events during hominin evolution after our common ancestor with the chimpanzee. SIGLEC13 was deleted by an Alu-mediated recombination event, and a single base pair deletion disrupted the ORF of SIGLEC17. Siglec-13 is expressed on chimpanzee monocytes, innate immune cells that react to bacteria. The human SIGLEC17P pseudogene mRNA is still expressed at high levels in human natural killer cells, which bridge innate and adaptive immune responses. As both resulting pseudogenes are homozygous in all human populations, we resurrected the originally encoded proteins and examined their functions. Chimpanzee Siglec-13 and the resurrected human Siglec-17 recruit a signaling adapter and bind sialic acids. Expression of either Siglec in innate immune cells alters inflammatory cytokine secretion in response to Toll-like receptor-4 stimulation. Both Siglecs can also be engaged by two potentially lethal sialylated bacterial pathogens of newborns and infants, agents with a potential impact on reproductive fitness. Neanderthal and Denisovan genomes show human-like sequences at both loci, corroborating estimates that the initial pseudogenization events occurred in the common ancestral population of these hominins. Both loci also show limited polymorphic diversity, suggesting selection forces predating the origin of modern humans. Taken together, these data suggest that genetic elimination of Siglec-13 and/or Siglec-17 represents signatures of infectious and/or other inflammatory selective processes contributing to population restrictions during hominin origins.

The Microcephalin Ancestral Allele in a Neanderthal Individual

Background The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. Methodology/Principal Findings Here we report the first PCR amplification and high- throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. Conclusions/Significance The MCPH1 genotype of the Monti Lessini (MLS) Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA.

Possible interbreeding in late Italian Neanderthals? New data from the Mezzena jaw (Monti Lessini, Verona, Italy).

In this article we examine the mandible of Riparo Mezzena a Middle Paleolithic rockshelter in the Monti Lessini (NE Italy, Verona) found in 1957 in association with Charentian Mousterian lithic assemblages. Mitochondrial DNA analysis performed on this jaw and on other cranial fragments found at the same stratigraphic level has led to the identification of the only genetically typed Neanderthal of the Italian peninsula and has confirmed through direct dating that it belongs to a late Neanderthal. Our aim here is to re-evaluate the taxonomic affinities of the Mezzena mandible in a wide comparative framework using both comparative morphology and geometric morphometrics. The comparative sample includes mid-Pleistocene fossils, Neanderthals and anatomically modern humans. This study of the Mezzena jaw shows that the chin region is similar to that of other late Neanderthals which display a much more modern morphology with an incipient mental trigone (e.g. Spy 1, La Ferrassie, Saint-Césaire). In our view, this change in morphology among late Neanderthals supports the hypothesis of anatomical change of late Neanderthals and the hypothesis of a certain degree of interbreeding with AMHs that, as the dating shows, was already present in the European territory. Our observations on the chin of the Mezzena mandible lead us to support a non abrupt phylogenetic transition for this period in Europe.

Alimenti vegetali a Bilancino e a Kostienki 16: il progetto dell'IIPP "Le risorse vegetali nel Paleolitico"

The background to the Project is set by a number of studies, currently being carried out in the Bilancino Gravettian site near Florence by some of the proponents of the project; these have led to the discovery of evidence of vegetable remains on lithic implements/artifacts (Noailles Burins and grindstone). The Project aims to apply new non-destructive techniques for the recovery and the identification of vegetable remains in Palaeolithic sites, in particular, the project focus on tools made from unknapped stone likely to be used in the treatment of plant-substances, such as pestles, grinders, grindstone, hearth-stones, etc. with the aim to acquire new evidence on the importance of the use of plants in the Palaeolithic and gain a better understanding of the economy and the diet of these most ancient humans. The procedure to analyze sediments eventually preserved on utilized pebbles is absolutely not invasive. Amog the numerous pebbles selected from the most important Italian Paleolithic sites only a grindstone and a pestle-grinder from Bilancino and a pestle-grinder from Kostenki have given starch residues. The discovery in Italy and Russia of a technique for the production of vegetable flour during the early phases of the Upper Paleolithic provides new evidence of a polycentric origin of such innovation anticipating by over 20,000 years the so-called Neolithic Revolution. The results obtained are also encouraging the systematic search for microresidues of vegetable origin in Paleolithic sites: for this aim we propose a protocol about the sampling and analysis modalities of vegetal residue from excavation to laboratory.