Dejana Brajković

Targeted retrieval and analysis of five Neandertal mtDNA genomes

Economic Ancient DNA Sequencing Analysis of ancient DNA is often limited by the availability of ancient material for sequencing. Briggs et al. (p. 318; see the news story by Pennisi) describe a method of ancient DNA sequence retrieval that greatly reduces shotgun sequencing costs while avoiding the many difficulties associated with direct PCR-based approaches. They generated five complete and one near-complete Neandertal mitochondrial DNA genomes, which would have been economically impossible with a simple shotgun approach. Analysis of these genomes shows that Neandertal populations had a much smaller effective population size than modern humans or great apes. Targeted sequencing improves Neandertal mitochondrial DNA retrieval and reveals low diversity among individuals. Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes.

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from approximately 0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 +/- 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.

Ancient gene flow from early modern humans into Eastern Neanderthals

It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.

Patterns of coding variation in the complete exomes of three Neandertals

Significance We use a hybridization approach to enrich the DNA from the protein-coding fraction of the genomes of two Neandertal individuals from Spain and Croatia. By analyzing these two exomes together with the genome sequence of a Neandertal from Siberia we show that the genetic diversity of Neandertals was lower than that of present-day humans and that the pattern of coding variation suggests that Neandertal populations were small and isolated from one another. We also show that genes involved in skeletal morphology have changed more than expected on the Neandertal evolutionary lineage whereas genes involved in pigmentation and behavior have changed more on the modern human lineage. We present the DNA sequence of 17,367 protein-coding genes in two Neandertals from Spain and Croatia and analyze them together with the genome sequence recently determined from a Neandertal from southern Siberia. Comparisons with present-day humans from Africa, Europe, and Asia reveal that genetic diversity among Neandertals was remarkably low, and that they carried a higher proportion of amino acid-changing (nonsynonymous) alleles inferred to alter protein structure or function than present-day humans. Thus, Neandertals across Eurasia had a smaller long-term effective population than present-day humans. We also identify amino acid substitutions in Neandertals and present-day humans that may underlie phenotypic differences between the two groups. We find that genes involved in skeletal morphology have changed more in the lineage leading to Neandertals than in the ancestral lineage common to archaic and modern humans, whereas genes involved in behavior and pigmentation have changed more on the modern human lineage.

First Epigravettian ceramic figurines from Europe (Vela Spila, Croatia).

Recent finds of 36 ceramic artifacts from the archaeological site of Vela Spila, Croatia, offer the first evidence of ceramic figurative art in late Upper Palaeolithic Europe, c. 17,500–15,000 years before present (BP). The size and diversity of this artistic ceramic assemblage indicate the emergence of a social tradition, rather than more ephemeral experimentation with a new material. Vela Spila ceramics offer compelling technological and stylistic comparisons with the only other evidence of a developed Palaeolithic ceramic tradition found at the sites of Pavlov I and Dolní Věstonice I, in the Czech Republic, c. 31,000–27,000 cal BP. Because of the 10,000-year gap between the two assemblages, the Vela Spila ceramics are interpreted as evidence of an independent invention of this technology. Consequently, these artifacts provide evidence of a new social context in which ceramics developed and were used to make art in the Upper Palaeolithic.

Revision of the Ungulate Fauna and Upper Pleistocene Stratigraphy of Veternica Cave (Zagreb, Croatia)

Revision of the Veternica ungulates removes Dama dama (L.) (fallow deer) and Megaceros giganteus (BLUMENBACH) (giant deer) from the species list and adds Bison priscus (BOJ ANUS) (bison) to it. The rhino remains do not allow a specific determination. A/ces a/ces (L.)(elk) and Capreolus capreolus (L.) (roe deer) are rarer than previously thought. Rupicapra rupicapra (L.) (chamois) remains are particularly common in levels d and h. Capra ibex (L.) (ibex) is limited to level d, while Sus scrofa (L.)(pig) needs to be added to the faunallist of level e. Cervus ela ph us (L. )(red deer) is the most common ungulate in all of the levels, with the exception of level d and perhaps level h. This revision remove s all of the socalled warm period ungulates from the fauna and casts doubt on an interglacial date for level j. Therefore, we suggest that level j at Veternica does not date to the last interglacial maximum (oxygen isotope sub-stage Se, e. 128-118,000 BP), but to a later and cooler time period with a more open environment. The sediments, however, do indicate relatively warm and wet conditions of deposition, at least with regards to the rest of the profile. We favor a date during sub-stages Sc or Sa (e. 100,000 and 80,000 BP, respectively), but leave the question open for the time being.