On the origin of our species

Craniometric variation and the ancestry of modern humans

OBJECTIVES

Ancient and contemporary DNA provide information about geographic variation in the ancestry of present-day humans. All living populations have ancestry from early Homo sapiens originating in sub-Saharan Africa. Populations of Eurasian descent also have a small amount of Neandertal ancestry. This study examines whether craniometric distances between recent modern human samples reflect this geographic variation in ancestry. Among recent modern humans, Eurasians are expected to be more similar to Neandertals, whereas both sub-Saharan Africans and Eurasians are expected to be equidistant from early H. sapiens.

MATERIALS AND METHODS

Data on 33 craniometric traits from 2524 recent modern humans were compared with data from the literature for Neandertals and early H. sapiens. Mahalanobis distances were computed for each modern specimen to both the Neandertal and early H. sapiens means. These distances were examined for differences between recent humans from sub-Saharan Africa (N = 373) and those of Eurasian descent (N = 2151).

RESULTS

Eurasians as a group are significantly closer than sub-Saharan Africans to Neandertals. There is no significant difference between the distances of sub-Saharan Africans and Eurasians to early H. sapiens.

DISCUSSION

The differences between sub-Saharan Africans and Eurasians for both Neandertals and early H. sapiens are as expected. Although there has been geographic differentiation among recent modern humans, including differences in Neandertal admixture, these differences have not affected overall similarity of recent modern sub-Saharan Africans and Eurasians to the earliest samples of H. sapiens.

Multiomic Insights into Human Health: Gut Microbiomes of Hunter-Gatherer, Agropastoral, and Western Urban Populations

Societies with exposure to preindustrial diets exhibit improved markers of health. Our study used a comprehensive multi-omic approach to reveal that the gut microbiome of the Ju/'hoansi hunter-gatherers, one of the most remote KhoeSan groups, exhibit a higher diversity and richness, with an abundance of microbial species lost in the western population. The Ju/'hoansi microbiome showed enhanced global transcription and enrichment of complex carbohydrate metabolic and energy generation pathways. The Ju/'hoansi also show high abundance of short-chain fatty acids that are associated with health and optimal immune function. In contrast, these pathways and their respective species were found in low abundance or completely absent in Western populations. Amino acid and fatty acid metabolism pathways were observed prevalent in the Western population, associated with biomarkers of chronic inflammation. Our study provides the first in-depth multi-omic characterization of the Ju/'hoansi microbiome, revealing uncharacterized species and functional pathways that are associated with health.

Reconstructing contact and a potential interbreeding geographical zone between Neanderthals and anatomically modern humans

While the interbreeding of Homo neanderthalensis (hereafter Neanderthal) and Anatomically modern human (AMH) has been proven, owing to the shortage of fossils and absence of appropriate DNA, the timing and geography of their interbreeding are not clearly known. In this study, we applied ecological niche modelling (maximum entropy approach) and GIS to reconstruct the palaeodistribution of Neanderthals and AMHs in Southwest Asia and Southeast Europe and identify their contact and potential interbreeding zone during marine isotope stage 5 (MIS 5), when the second wave of interbreeding occurred. We used climatic variables characterizing the environmental conditions of MIS 5 ca. 120 to 80 kyr (averaged value) along with the topography and coordinates of Neanderthal and modern human archaeological sites to characterize the palaeodistribution of each species. Overlapping the models revealed that the Zagros Mountains were a contact and potential interbreeding zone for the two human species. We believe that the Zagros Mountains acted as a corridor connecting the Palearctic/Afrotropical realms, facilitating northwards dispersal of AMHs and southwards dispersal of Neanderthals during MIS 5. Our analyses are comparable with archaeological and genetic evidence collected during recent decades.

Evolved Open-Endedness in Cultural Evolution: A New Dimension in Open-Ended Evolution Research

The goal of Artificial Life research, as articulated by Chris Langton, is "to contribute to theoretical biology by locating life-as-we-know-it within the larger picture of life-as-it-could-be." The study and pursuit of open-ended evolution in artificial evolutionary systems exemplify this goal. However, open-ended evolution research is hampered by two fundamental issues: the struggle to replicate open-endedness in an artificial evolutionary system and our assumption that we only have one system (genetic evolution) from which to draw inspiration. We argue not only that cultural evolution should be seen as another real-world example of an open-ended evolutionary system but that the unique qualities seen in cultural evolution provide us with a new perspective from which we can assess the fundamental properties of, and ask new questions about, open-ended evolutionary systems, especially with regard to evolved open-endedness and transitions from bounded to unbounded evolution. Here we provide an overview of culture as an evolutionary system, highlight the interesting case of human cultural evolution as an open-ended evolutionary system, and contextualize cultural evolution by developing a new framework of (evolved) open-ended evolution. We go on to provide a set of new questions that can be asked once we consider cultural evolution within the framework of open-ended evolution and introduce new insights that we may be able to gain about evolved open-endedness as a result of asking these questions.

Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years

Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.

On Language Cognition Relations and Evolution of Language

One can understand the importance of language with its relation to mental activities such as memory and thinking. Language, a crucial human ability, has long attracted the attention of various theorists and philosophers. Language, by its nature, interacts with many biological, cultural and psychological factors. This article has drawn a general framework by bringing together the views from disciplines such as linguistics, psychology, anthropology, biology and neuroscience. On the one hand, while the theoretical opinions about language are included, on the other hand, language is discussed in the context of the changes we went through by separating from our common ancestor in the evolution process. When dealing with language, it is possible to talk about our differences from animals, the interaction of language with our cognitive processes and its organization in the brain. The views put forward by philosophers such as Plato and Descartes about the relationship between language and cognitions have expanded by Chomsky, Pinker, Dunbar and others on the evolution of language. In this article, evolutionary psychology, which strives to understand language and its relationship with cognitions, is emphasized by combining the data of modern evolutionary biology and cognitive psychology. Language is acquired quickly and without the intense need for learning experiences, thanks to innate schemas, suggests that evolution formed these schemas. According to another view, the influence of the environment and culture gains importance instead of innatism. In addition, different opinions on the evolution of language are briefly discussed. Discussion topics include triggers of language development in evolution. These are related to biological and cultural influences, influences of vocalization and hand gestures on language. When thinking about language and its evolution, it is inevitable to observe and examine cognitive processes and thought. Multidisciplinary studies can also provide important information about the evolution of language while trying to understand the complex relationship between language and cognition.

Conserved mammalian modularity of quantitative trait loci revealed human functional orthologs in blood pressure control

Genome-wide association studies (GWAS) have routinely detected human quantitative trait loci (QTLs) for complex traits. Viewing that most GWAS single nucleotide polymorphisms (SNPs) are found in non-coding regions unrelated to the physiology of a polygenic trait of interest, a vital question to answer is whether or not any of these SNPs can functionally alter the phenotype with which it is associated. The study of blood pressure (BP) is a case in point. Conserved mechanisms in controlling BP by modularity is now unifying differing mammalian orders in that understanding mechanisms in rodents is tantamount to revealing the same in humans, while overcoming experimental limitations imposed by human studies. As a proof of principle, we used BP QTLs from Dahl salt-sensitive rats (DSS) as substitutes to capture distinct human functional orthologs. 3 DSS BP QTLs are located into distinct genome regions and correspond to several human GWAS genes. Each of the QTLs independently exerted a major impact on BP in vivo. BP was functionally changed by normotensive alleles from each of these QTLs, and yet, the human GWAS SNPs do not exist in the rat. They cannot be responsible for physiological alterations in BP caused by these QTLs. These SNPs are genome emblems for QTLs nearby, rather than being QTLs per se, since they only emerged during primate evolution after BP-regulating mechanisms have been established. We then identified specific mutated coding domains that are conserved between rodents and humans and that may implicate different steps of a common pathway or separate pathways.

Functional Captures of Multiple Human Quantitative Trait Loci Regulating Blood Pressure with the Use of Orthologs in Genetically Defined Rat Models

BACKGROUND

Most signals from human genome-wide association studies (GWAS) for blood pressure (BP) are single-nucleotide polymorphisms (SNPs). It was unknown if such SNPs can functionally affect BP. Because BP is similar between humans and rodents, unraveling basic mechanisms from rodents can reveal the same BP-modulating mechanisms in humans originating from their common ancestors while overcoming limitations in human epidemiology.

METHODS

For the first time, we used quantitative trait loci (QTLs) from Dahl salt-sensitive (DSS) rats as functional surrogates to capture human BP QTLs.

RESULTS

A total of 107 human GWAS genes may be classified into 2 common pathways of hypertension pathogeneses. Among them, 4 DSS BP QTLs correspond to 4 human GWAS genes. Each of them independently showed a major impact on BP in vivo and thus functional redundancy. BP was altered by each of these 4 QTLs, but human GWAS SNPs marking these QTLs do not exist in the rat. They cannot be responsible for physiological changes in BP caused by these QTLs and are genome signposts marking positions of the QTLs nearby, rather than being QTLs themselves. These SNPs appeared during primate evolution, independently of BP regulation. Because the functional dosage of QTLs, not their gene dose, determined hypertension pathogenesis, a role for the noncoding GWAS SNPs in BP via regulating gene expressions can be discounted.

CONCLUSIONS

The human QTLs may function in a common pathway, with each involved in a different step in the pathway leading to BP control. These results may be conceptually paradigm shifting.

Dynamics of a birth-death process based on combinatorial innovation

A feature of human creativity is the ability to take a subset of existing items (e.g. objects, ideas, or techniques) and combine them in various ways to give rise to new items, which, in turn, fuel further growth. Occasionally, some of these items may also disappear (extinction). We model this process by a simple stochastic birth-death model, with non-linear combinatorial terms in the growth coefficients to capture the propensity of subsets of items to give rise to new items. In its simplest form, this model involves just two parameters (P, α). This process exhibits a characteristic 'hockey-stick' behaviour: a long period of relatively little growth followed by a relatively sudden 'explosive' increase. We provide exact expressions for the mean and variance of this time to explosion and compare the results with simulations. We then generalise our results to allow for more general parameter assignments, and consider possible applications to data involving human productivity and creativity.

Human origins in a southern African palaeo-wetland and first migrations

Anatomically modern humans originated in Africa around 200 thousand years ago (ka)^1-4. Although some of the oldest skeletal remains suggest an eastern African origin², southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny^5,6. Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1'2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi-Okavango palaeo-wetland of southern Africa⁷, approximately 200 ka (95% confidence interval, 240-165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast-southwest dispersal between 130 and 110 ka. Palaeo-climate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to a sustained effective population size (L0k), whereas wet-dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1'2), as supported by extensive south-coastal archaeological evidence^8-10. Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes.

Prospects of genetic testing for steroid-resistant nephrotic syndrome in Nigerian children: a narrative review of challenges and opportunities

The prevalence of childhood steroid-resistant nephrotic syndrome (SRNS) ranges from 35% to 92%. This steroid resistance among Nigerian children also reflects underlying renal histopathology, revealing a rare minimal-change disease and a varying burden of membranoproliferative glomerulonephritis and focal segmental glomerulosclerosis (FSGS). FSGS tends to progress to end-stage kidney disease, which requires dialysis and/or renal transplantation. While knowledge of the molecular basis of NS is evolving, recent data support the role of mutant genes that otherwise maintain the structural and functional composition of the glomerular filtration barrier to account for many monogenic forms of FSGS. With the advent of next-generation sequencing, >39 genes are currently associated with SRNS, and the number is likely to increase in the near future. Monogenic FSGS is primarily resistant to steroids, and this foreknowledge obviates the need for steroids, other immunosuppressive therapy, and renal biopsy. Therefore, a multidisciplinary collaboration among cell biologists, molecular physiologists, geneticists, and clinicians holds prospects of fine-tuning the management of SRNS caused by known mutant genes. This article describes the genetics of NS/SRNS in childhood and also gives a narrative review of the challenges and opportunities for molecular testing among children with SRNS in Nigeria. For these children to benefit from genetic diagnosis, Nigeria must aspire to have and develop the manpower and infrastructure required for medical genetics and genomic medicine, leveraging on her existing experiences in genomic medicine. Concerted efforts can be put in place to increase the number of enrollees in Nigeria’s National Health Insurance Scheme (NHIS). The scope of the NHIS can be expanded to cater for the expensive bill of genetic testing within or outside the structure of the National Renal Care Policy proposed by Nigerian nephrologists.

A dispersal of Homo sapiens from southern to eastern Africa immediately preceded the out-of-Africa migration

Africa was the birth-place of Homo sapiens and has the earliest evidence for symbolic behaviour and complex technologies. The best-attested early flowering of these distinctive features was in a glacial refuge zone on the southern coast 100–70 ka, with fewer indications in eastern Africa until after 70 ka. Yet it was eastern Africa, not the south, that witnessed the first major demographic expansion, ~70–60 ka, which led to the peopling of the rest of the world. One possible explanation is that important cultural traits were transmitted from south to east at this time. Here we identify a mitochondrial signal of such a dispersal soon after ~70 ka – the only time in the last 200,000 years that humid climate conditions encompassed southern and tropical Africa. This dispersal immediately preceded the out-of-Africa expansions, potentially providing the trigger for these expansions by transmitting significant cultural elements from the southern African refuge.

[Genetics and origin of Homo sapiens]

Usually, paleoanthropology studies remains and artefacts. However, more recently, genetics offer new avenues. Information on humanisation mechanisms has been obtained from comparison with primate or archaic Homo DNA sequences. Likewise, the 1 000 Genomes Project has characterized the geographic spectrum of human genetic variation offering a basis for a genomic study of Homo sapiens phylogeny. From these studies, a model, Out of Africa, was derived. His origin is Africa, where he lived 200 000 years ago. A small fraction of the population left Africa between 50 and 100 000 years ago that have populated the rest of the world, to Europe, coastal Asia to Australia and mainland Asia to Behring Land Bridge and America. The model is supported by the decrease of genetic diversity with the distance to Eastern Africa (serial founder effect). In Europe and Asia, Homo sapiens met archaic Homo neanderthalis and H denisova. The presence of 1-3% neanderthalis sequences in modern Homo ADN indicates admixtures between these groups. Some archaic sequences are on positive selection pressure, thus suggesting that the extinct hominins might have facilitated the adaptation of H sapiens to new environments.

Culture and art: Importance of art practice, not aesthetics, to early human culture

Art is expressed in multiple formats in today's human cultures. Physical traces of stone tools and other archaeological landmarks suggest early nonart cultural behavior and symbolic cognition in the early Homo sapiens (HS) who emerged ~300,000-200,000 years ago in Africa. Fundamental to art expression is the neural underpinning for symbolic cognition, and material art is considered its prime example. However, prior to producing material art, HS could have exploited symbolically through art-rooted biological neural pathways for social purpose, namely, those controlling interpersonal motoric coordination and sound codependence. Aesthetics would not have been the primary purpose; arguments for group dance and rhythmical musical sounds are offered here. In addition, triggers for symbolic body painting are discussed. These cultural art formats could well have preceded material art and would have enhanced unity, inclusiveness, and cooperative behavior, contributing significantly to already existing nonart cultural practices.

The evolution of modern human brain shape

Modern humans have large and globular brains that distinguish them from their extinct Homo relatives. The characteristic globularity develops during a prenatal and early postnatal period of rapid brain growth critical for neural wiring and cognitive development. However, it remains unknown when and how brain globularity evolved and how it relates to evolutionary brain size increase. On the basis of computed tomographic scans and geometric morphometric analyses, we analyzed endocranial casts of Homo sapiens fossils (N = 20) from different time periods. Our data show that, 300,000 years ago, brain size in early H. sapiens already fell within the range of present-day humans. Brain shape, however, evolved gradually within the H. sapiens lineage, reaching present-day human variation between about 100,000 and 35,000 years ago. This process started only after other key features of craniofacial morphology appeared modern and paralleled the emergence of behavioral modernity as seen from the archeological record. Our findings are consistent with important genetic changes affecting early brain development within the H. sapiens lineage since the origin of the species and before the transition to the Later Stone Age and the Upper Paleolithic that mark full behavioral modernity.