Neandertal genome: the ins and outs of African genetic diversity

Human genetics and molecular genomics of Chiari malformation type 1

Chiari malformation type 1 (CM1) is the most common structural brain disorder involving the craniocervical junction, characterized by caudal displacement of the cerebellar tonsils below the foramen magnum into the spinal canal. Despite the heterogeneity of CM1, its poorly understood patho-etiology has led to a 'one-size-fits-all' surgical approach, with predictably high rates of morbidity and treatment failure. In this review we present multiplex CM1 families, associated Mendelian syndromes, and candidate genes from recent whole exome sequencing (WES) and other genetic studies that suggest a significant genetic contribution from inherited and de novo germline variants impacting transcription regulation, craniovertebral osteogenesis, and embryonic developmental signaling. We suggest that more extensive WES may identify clinically relevant, genetically defined CM1 subtypes distinguished by unique neuroradiographic and neurophysiological endophenotypes.

On the antiquity of language: the reinterpretation of Neandertal linguistic capacities and its consequences

It is usually assumed that modern language is a recent phenomenon, coinciding with the emergence of modern humans themselves. Many assume as well that this is the result of a single, sudden mutation giving rise to the full "modern package." However, we argue here that recognizably modern language is likely an ancient feature of our genus pre-dating at least the common ancestor of modern humans and Neandertals about half a million years ago. To this end, we adduce a broad range of evidence from linguistics, genetics, paleontology, and archaeology clearly suggesting that Neandertals shared with us something like modern speech and language. This reassessment of the antiquity of modern language, from the usually quoted 50,000-100,000 years to half a million years, has profound consequences for our understanding of our own evolution in general and especially for the sciences of speech and language. As such, it argues against a saltationist scenario for the evolution of language, and toward a gradual process of culture-gene co-evolution extending to the present day. Another consequence is that the present-day linguistic diversity might better reflect the properties of the design space for language and not just the vagaries of history, and could also contain traces of the languages spoken by other human forms such as the Neandertals.

Ancestry of modern Europeans: contributions of ancient DNA

Understanding the peopling history of Europe is crucial to comprehend the origins of modern populations. Of course, the analysis of current genetic data offers several explanations about human migration patterns which occurred on this continent, but it fails to explain precisely the impact of each demographic event. In this context, direct access to the DNA of ancient specimens allows the overcoming of recent demographic phenomena, which probably highly modified the constitution of the current European gene pool. In recent years, several DNA studies have been successfully conducted from ancient human remains thanks to the improvement of molecular techniques. They have brought new fundamental information on the peopling of Europe and allowed us to refine our understanding of European prehistory. In this review, we will detail all the ancient DNA studies performed to date on ancient European DNA from the Middle Paleolithic to the beginning of the protohistoric period.

Archaic human genomics

For much of the 20th century, the predominant view of human evolutionary history was derived from the fossil record. Homo erectus was seen arising in Africa from an earlier member of the genus and then spreading throughout the Old World and into the Oceania. A regional continuity model of anagenetic change from H. erectus via various intermediate archaic species into the modern humans in each of the regions inhabited by H. erectus was labeled the multiregional model of human evolution (MRE). A contrasting model positing a single origin, in Africa, of anatomically modern H. sapiens with some populations later migrating out of Africa and replacing the local archaic populations throughout the world with complete replacement became known as the recent African origin (RAO) model. Proponents of both models used different interpretations of the fossil record to bolster their views for decades. In the 1980s, molecular genetic techniques began providing evidence from modern human variation that allowed not only the different models of modern human origins to be tested but also the exploration demographic history and the types of selection that different regions of the genome and even specific traits had undergone. The majority of researchers interpreted these data as strongly supporting the RAO model, especially analyses of mitochondrial DNA (mtDNA). Extrapolating backward from modern patterns of variation and using various calibration points and substitution rates, a consensus arose that saw modern humans evolving from an African population around 200,000 years ago. Much later, around 50,000 years ago, a subset of this population migrated out of Africa replacing Neanderthals in Europe and western Asia as well as archaics in eastern Asia and Oceania. mtDNA sequences from more than two-dozen Neanderthals and early modern humans re-enforced this consensus. In 2010, however, the complete draft genomes of Neanderthals and of heretofore unknown hominins from Siberia, called Denisovans, demonstrated gene flow between these archaic human species and modern Eurasians but not sub-Saharan Africans. Although the levels of gene flow may be very limited, this unexpected finding does not fit well with either the RAO model or MRE model. More thorough sampling of modern human diversity, additional fossil discoveries, and the sequencing of additional hominin fossils are necessary to throw light onto our origins and our history.

Human pelvis and long bones reveal differential preservation of ancient population history and migration out of Africa

One of the main events in the history of our species has been our expansion out of Africa. A clear signature of this expansion has been found on global patterns of neutral genetic variation, whereby a serial founder effect accompanied the colonization of new regions, in turn creating a wilhin-pupulation decrease in neutral genetic diversity with increasing distance from Africa. This same distinctive pattern has also been described for cranial and dental morphological variation in human populations distributed across the globe. Here, we used a data set of postcranial linear measurements for 30 globally distributed human populations, and a climatic data set of minimum annual temperature, maximum annual temperature, and precipitation in order to separate for the first time the relative effect of neutral demographic processes and climatic selection on four long (limb) bones (femur, tibia, radius, and humerus) versus the pelvic bones of the human appendicular skeleton. We implemented a stepwise regression procedure in which phenotypic variance is assumed to be affected by the iterative founder events that accompanied human expansion from Africa, as well as by climate. This model included, as independent factors, geographic distance from central Africa, the three climatic variables, and all possible interactions between the three climatic variables. We excluded all nonsignificant factors by backward stepwise elimination with the aim of identifying the minimal model significantly explaining variation in the phenotypic data. Our results indicate a sharp difference in the way the pelvis and the limb bones reflect the neutral signature of the out-of-Africa expansion. Consistent with previous analyses of the cranium and dentition, pelvic shape variation shows a significant within-population decrease with increasing distance from Africa. However, no such pattern could be found in the long bones. Rather, in the case of both the tibia and the femur, a significant relationship between population-level variance and minimum temperature was demonstrated. Hence, in the case of these limb bones, it is probable that the effects of climatic selection have obliterated the demographic signature of human dispersal from Africa. Our finding mat pelvic variation exhibits the neutral effects of demographic history suggests that consideration of this skeletal element might be used to shed light on factors of human population history, just as the cranium has done.

The great human expansion

Genetic and paleoanthropological evidence is in accord that today's human population is the result of a great demic (demographic and geographic) expansion that began approximately 45,000 to 60,000 y ago in Africa and rapidly resulted in human occupation of almost all of the Earth's habitable regions. Genomic data from contemporary humans suggest that this expansion was accompanied by a continuous loss of genetic diversity, a result of what is called the "serial founder effect." In addition to genomic data, the serial founder effect model is now supported by the genetics of human parasites, morphology, and linguistics. This particular population history gave rise to the two defining features of genetic variation in humans: genomes from the substructured populations of Africa retain an exceptional number of unique variants, and there is a dramatic reduction in genetic diversity within populations living outside of Africa. These two patterns are relevant for medical genetic studies mapping genotypes to phenotypes and for inferring the power of natural selection in human history. It should be appreciated that the initial expansion and subsequent serial founder effect were determined by demographic and sociocultural factors associated with hunter-gatherer populations. How do we reconcile this major demic expansion with the population stability that followed for thousands years until the inventions of agriculture? We review advances in understanding the genetic diversity within Africa and the great human expansion out of Africa and offer hypotheses that can help to establish a more synthetic view of modern human evolution.

Paleogenomics of archaic hominins

In order to understand the genetic basis for the evolutionary success of modern humans, it is necessary to compare their genetic makeup to that of closely related species. Unfortunately, our closest living relatives, the chimpanzees, are evolutionarily quite distant. With the advent of ancient DNA study and more recently paleogenomics - the study of the genomes of ancient organisms - it has become possible to compare human genomes to those of much more closely related groups. Our closest known relatives are the Neanderthals, which evolved and lived in Europe and Western Asia, from about 600,000 years ago until their disappearance around 30,000 years ago following the expansion of anatomically modern humans into their range. The closely related Denisovans are only known by virtue of their DNA, which has been extracted from bone fragments dating around 30,000 to 50,000 years ago found in a single Siberian cave. Analyses of Neanderthal and Denisovan nuclear and mitochondrial genomes have revealed surprising insights into these archaic humans as well as our own species. The genomes provide a preliminary catalogue of derived amino acids that are specific to all extant modern humans, thus offering insights into the functional differences between the three lineages. In addition, the genomes provide evidence of gene flow between the three lineages after anatomically modern humans left Africa, drastically changing our view of human evolution.

Archaic human ancestry in East Asia

Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome--a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.

People of the ancient rainforest: late Pleistocene foragers at the Batadomba-lena rockshelter, Sri Lanka

Batadomba-lena, a rockshelter in the rainforest of southwestern Sri Lanka, has yielded some of the earliest evidence of Homo sapiens in South Asia. H. sapiens foragers were present at Batadomba-lena from ca. 36,000 cal BP to the terminal Pleistocene and Holocene. Human occupation was sporadic before the global Last Glacial Maximum (LGM). Batadomba-lena's Late Pleistocene inhabitants foraged for a broad spectrum of plant and mainly arboreal animal resources (monkeys, squirrels and abundant rainforest snails), derived from a landscape that retained equatorial rainforest cover through periods of pronounced regional aridity during the LGM. Juxtaposed hearths, palaeofloors with habitation debris, postholes, excavated pits, and animal and plant remains, including abundant Canarium nutshells, reflect intensive habitation of the rockshelter in times of monsoon intensification and biome reorganisation after ca. 16,000 cal BP. This period corresponds with further broadening of the economic spectrum, evidenced though increased contribution of squirrels, freshwater snails and Canarium nuts in the diet of the rockshelter occupants. Microliths are more abundant and morphologically diverse in the earliest, pre-LGM layer and decline markedly during intensified rockshelter use on the wane of the LGM. We propose that changing toolkits and subsistence base reflect changing foraging practices, from shorter-lived visits of highly mobile foraging bands in the period before the LGM, to intensified use of Batadomba-lena and intense foraging for diverse resources around the site during and, especially, following the LGM. Traces of ochre, marine shell beads and other objects from an 80 km-distant shore, and, possibly burials reflect symbolic practices from the outset of human presence at the rockshelter. Evidence for differentiated use of space (individual hearths, possible habitation structures) is present in LGM and terminal Pleistocene layers. The record of Batadomba-lena demonstrates that Late Pleistocene pathways to (aspects of) behavioural 'modernity' (composite tools, practice of symbolism and ritual, broad spectrum economy) were diverse and ecologically contingent.

An X-linked haplotype of Neandertal origin is present among all non-African populations

Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of Homo sapiens who left Africa between 80 and 50 Kya (thousand years ago) to colonize the rest of the world. Here, we provide evidence of a notable presence (9% overall) of a Neandertal-derived X chromosome segment among all contemporary human populations outside Africa. Our analysis of 6,092 X-chromosomes from all inhabited continents supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans. It indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.

Genetic diversity in India and the inference of Eurasian population expansion

Background

Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored.

Results

To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90 to 110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans.

Conclusions

Our results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia.