Identification of genes involved in the evolution of human intelligence through combination of inter-species and intra-species genetic variations

Understanding the evolution of human intelligence is an important undertaking in the science of human genetics. A great deal of biological research has been conducted to search for genes which are related to the significant increase in human brain volume and cerebral cortex complexity during hominid evolution. However, genetic changes affecting intelligence in hominid evolution have remained elusive. We supposed that a subset of intelligence-related genes, which harbored intra-species variations in human populations, may also be evolution-related genes which harbored inter-species variations between humans (Homo sapiens) and great apes (including Pan troglodytes and Pongo abelii). Here we combined inter-species and intra-species genetic variations to discover genes involved in the evolution of human intelligence. Information was collected from published GWAS works on intelligence and a total of 549 genes located within the intelligence-associated loci were identified. The intelligence-related genes containing human-specific variations were detected based on the latest high-quality genome assemblies of three human’s closest species. Finally, we identified 40 strong candidates involved in human intelligence evolution. Expression analysis using RNA-Seq data revealed that most of the genes displayed a relatively high expression in the cerebral cortex. For these genes, there is a distinct expression pattern between humans and other species, especially in neocortex tissues. Our work provided a list of strong candidates for the evolution of human intelligence, and also implied that some intelligence-related genes may undergo inter-species evolution and contain intra-species variation.

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions

ABSTRACT Bacteria associated with eukaryotic hosts can affect host fitness and trophic interactions between eukaryotes, but the extent to which bacteria influence the eukaryotic species interactions within trophic levels that modulate biodiversity and species coexistence is mostly unknown. Here, we used phytoplankton, which are a classic model for evaluating interactions between species, grown with and without associated bacteria to test whether the bacteria alter the strength and type of species interactions within a trophic level. We demonstrate that host-associated bacteria alter host growth rates and carrying capacity. This did not change the type but frequently changed the strength of host interspecific interactions by facilitating host growth in the presence of an established species. These findings indicate that microbiomes can regulate their host species’ interspecific interactions. As between-species interaction strength impacts their ability to coexist, our findings show that microbiomes have the potential to modulate eukaryotic species diversity and community composition. IMPORTANCE Description of the Earth’s microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

DOES EVOLUTIONARY BIOLOGY HELP THE UNDERSTANDING OF METABOLIC SURGERY? A FOCUSED REVIEW

ABSTRACT Introduction: The wide net of physiological issues involved in metabolic surgery is extremely complex. Nonetheless, compared anatomy and phisiology can provide good clues of how digestive tracts are shaped for more or less caloric food, for more or less fiber, for abundance and for scarcity. Objective: To review data from Compared Anatomy and Physiology, and in the Evolutionary Sciences that could help in the better comprehension of the metabolic surgery. Method: A focused review of the literature selecting information from these three fields of knowledge in databases: Cochrane Library, Medline and SciELO, articles and book chapters in English and Portuguese, between 1955 and 2019, using the headings “GIP, GLP-1, PYY, type 2 diabetes, vertebrates digestive system, hominid evolution, obesity, bariatric surgery “. Results: The digestive tract of superior animals shows highly specialized organs to digest and absorb specific diets. In spite of the wide variations of digestive systems, some general rules are observed. The proximal part of the digestive tract, facing the scarcity of sugars, is basically dedicated to generate sugar from different substrates (gluconeogenesis). Basic proximal gut tasks are to proportionally input free sugars, insulin, other fuels and to generate anabolic elements to the blood, some of them obesogenic. To limit the ingestion by satiety, by gastric emptying diminution and to limit the excessive elevation of major fuels (sugar and fat) in the blood are mostly the metabolict asks of the distal gut. A rapid and profound change in human diet composition added large amounts of high glycemic index foods. They seem to have caused an enhancement in the endocrine and metabolic activities of the proximal gut and a reduction in these activities of the distal gut. The most efficient models of metabolic surgery indeed make adjustments in this proximal/distal balance in the gut metabolic activities. Conclusion: Metabolic surgery works basically by making adjustments to the proximal and distal gut metabolic activities that resemble the action of natural selection in the development the digestive systems of superior animals.

The Evolutionary Radiation of Hominids: a Phylogenetic Comparative Study

Over the last 150 years the diversity and phylogenetic relationships of the hominoids have been one of the main focuses in biological and anthropological research. Despite this, the study of factors involved in their evolutionary radiation and the origin of the hominin clade, a key subject for the further understanding of human evolution, remained mostly unexplored. Here we quantitatively approach these events using phylogenetic comparative methods and craniofacial morphometric data from extant and fossil hominoid species. Specifically, we explore alternative evolutionary models that allow us to gain new insights into this clade diversification process. Our results show a complex and variable scenario involving different evolutionary regimes through the hominid evolutionary radiation –modeled by Ornstein-Uhlenbeck multi-selective regime and Brownian motion multi-rate scenarios–. These different evolutionary regimes might relate to distinct ecological and cultural factors previously suggested to explain hominid evolution at different evolutionary scales along the last 10 million years.

Ice Age theory: a correspondence between Milutin Milanković and Vojislav Mišković

Ice Ages (IA) and their glacial periods can be regarded as significant natural hazards (NH). Unfortunately, the knowledge of hominid evolution that occurred during IAs, in such extreme climatic fluctuations, is preserved almost exclusively in mythology. The omission of more scientific discourse regarding the history of NH during IAs should be rectified for posterity. As our civilization will likely have to cope with the beginnings of a new glacial phase, a more complete understanding of the mechanisms of IA climate dynamics is crucial. This paper presents an unpublished correspondence between M. Milanković, a polymath and the founder of the Astronomical theory of Ice Ages (ATIA), and the astronomer V. Mišković, one of Milanković’s major contributors to the development of his theory. Additional insight related to the ATIA by M. Milanković is given, particularly regarding the succession of glacial and interglacial periods on Earth. In this completely preserved correspondence, taking place from 1924 until 1952, also reside letters concerning the research of M. Milanković and V. Mišković as it relates to the research of Alfred Wegener and Wladimir Köppen. These letters are on the topic of M. Milanković’s 1920’s work. At the Astronomical Observatory in Belgrade, M. Milanković found useful data in the observatory’s publications and orchestrated the numerical calculations he needed for his ATIA with V. Mišković aid.

Cyclic Hominid Evolution in A Moroccan-Algerian Coastal Refuge: The Last Million Years

To explain the abundance of species of genus Homo in the fossil record of Africa south of the Sahara, the small Moroccan-Algerian coastal zone that was isolated by the barren Sahara is proposed to have been a refuge in which cyclic evolution occurred. A dry climate in combination with a small population enabled natural selection to generate new sub species or species during each climate cycle. As generalized from the last two major glaciations, in each cycle three coastal zone climates of differing aridity occurred, depending on the latitudinal zonality of high latitude Gulf Stream flow. When initially isolated with minimal zonality (strong northward North Atlantic Drift of Gulf Stream water), the coastal climate was like today’s, with warm summers and mild winter rains. Subsequently during intervals of ice sheet growth with intermediate zonality (weaker Drift), winters were colder, the climate was drier, and the environmental stresses increased. Finally, with the quite strong or complete zonality associated with Northern Hemisphere deglaciations (little or no Drift), extreme aridity often reduced the inhabitable area of the coastal zone. When each Eurasian deglaciation was completed, the isolation was probably briefly interrupted, as it was in the mid Holocene, by a well-watered savanna that developed across the Sahara. The savannas enabled each small and genetically modified population to increase and extend its range southward into the larger Africa. The pulses of evolution are directly related to glacial cycles by way of Earth’s orbital eccentricity and precession of the equinox. The intervals of coastal zone isolation usually lasted almost 22,000 years, which is the time needed for the precession of the equinox to move summer around on Earth’s orbit from one perihelion point to the next where monsoons are strong, and deglaciation and the savannas tend to occur. However, isolations as long as ~76,000 years also are found in the record because Eurasian ice sheet growth sometimes resumed before deglaciation was complete. In the last million years there may have been at least 18 pluvial savanna intervals when populations of new species or sub species of hominids would have extended their range by expanding on the savanna into the larger Africa or Eurasia. Periodic pulses of evolution of primitive hominids probably also occurred much earlier in the Pliocene with brief savannas but without large Northern glaciations. Generation of new species of hominids in the coastal zone and their injection into the larger Africa by savanna connections may therefore have been largely responsible for the abundance of genus Homo and predecessors in the fossil record and for our own Homo sapiens that we know today.

Monsoon-driven Saharan dust variability over the past 240,000 years

Reconstructions of past Saharan dust deposition in marine sediments provide foundational records of North African climate over time scales of 103to 106years. Previous dust records show primarily glacial-interglacial variability in the Pleistocene, in contrast to other monsoon records showing strong precessional variability. Here, we present the first Saharan dust record spanning multiple glacial cycles obtained using230Th normalization, an improved method of calculating fluxes. Contrary to previous data, our record from the West African margin demonstrates high correlation with summer insolation and limited glacial-interglacial changes, indicating coherent variability in the African monsoon belt throughout the late Pleistocene. Our results demonstrate that low-latitude Saharan dust emissions do not vary synchronously with high- and mid-latitude dust emissions, and they call into question the use of existing Plio-Pleistocene dust records to investigate links between climate and hominid evolution.

Detection of a novel, primate-specific ‘kill switch’ tumor suppression mechanism that may fundamentally control cancer risk in humans: an unexpected twist in the basic biology of TP53

The activation of TP53 is well known to exert tumor suppressive effects. We have detected aprimate-specificadrenal androgen-mediated tumor suppression system in which circulating DHEAS is converted to DHEA specifically in cells in which TP53 has beeninactivated. DHEA is anuncompetitiveinhibitor of glucose-6-phosphate dehydrogenase (G6PD), an enzyme indispensable for maintaining reactive oxygen species within limits survivable by the cell. Uncompetitive inhibition is otherwise unknown in natural systems because it becomesirreversiblein the presence of high concentrations of substrate and inhibitor. In addition to primate-specific circulating DHEAS, a unique, primate-specific sequence motif that disables an activating regulatory site in the glucose-6-phosphatase (G6PC) promoter was also required to enable function of this previously unrecognized tumor suppression system. In human somatic cells, loss of TP53 thus triggers activation of DHEAS transport proteins and steroid sulfatase, which converts circulating DHEAS into intracellular DHEA, and hexokinase which increases glucose-6-phosphate substrate concentration. The triggering of these enzymes in the TP53-affected cell combines with the primate-specific G6PC promoter sequence motif that enables G6P substrate accumulation, driving uncompetitive inhibition of G6PD to irreversibility and ROS-mediated cell death. By this catastrophic ‘kill switch’ mechanism, TP53 mutations are effectively prevented from initiating tumorigenesis in the somatic cells of humans, the primate with the highest peak levels of circulating DHEAS. TP53 mutations in human tumors therefore represent fossils of kill switch failure resulting from an age-related decline in circulating DHEAS, a potentially reversible artifact of hominid evolution.