Hasil untuk "Human evolution"

T. Derrien, Rory Johnson, G. Bussotti et al.

The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths. In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences—particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain. Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs.

Martin H. Levinson

R. Cann, M. Stoneking, A. Wilson

Brian L. Hie, Varun R. Shanker, Duo Xu et al.

A general protein language model guides protein evolution with 20 or fewer variants needed for testing. Natural evolution must explore a vast landscape of possible sequences for desirable yet rare mutations, suggesting that learning from natural evolutionary strategies could guide artificial evolution. Here we report that general protein language models can efficiently evolve human antibodies by suggesting mutations that are evolutionarily plausible, despite providing the model with no information about the target antigen, binding specificity or protein structure. We performed language-model-guided affinity maturation of seven antibodies, screening 20 or fewer variants of each antibody across only two rounds of laboratory evolution, and improved the binding affinities of four clinically relevant, highly mature antibodies up to sevenfold and three unmatured antibodies up to 160-fold, with many designs also demonstrating favorable thermostability and viral neutralization activity against Ebola and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudoviruses. The same models that improve antibody binding also guide efficient evolution across diverse protein families and selection pressures, including antibiotic resistance and enzyme activity, suggesting that these results generalize to many settings.

G. Richards

Éléments de sociologie: textes choisis et ordonnés.Par Prof. C. Bouglé J. Raffault. (Publications du Centre de Documentation sociale.) Pp. viii + 506. (Paris: Félix Alcan, 1926.) 30 francs.

R. Wrangham

Sanchita Chakraborty, S.R. Rao, Abhijit Poddar

Mpox virus (MPXV) is the only pathogen that triggered two Public Health Emergency of International Concern (PHEIC) declarations, first in July 2022 and then again in August 2024. The 2022 outbreak was attributed primarily to clade IIb MPXV, specifically lineage B.1. However, the 2024 global outbreak was largely due to the emergence of clade Ib MPXV, which was first identified in the Sud Kivu region of the Democratic Republic of the Congo in 2023. During this period, the transmission route of MPXV transitioned from primarily zoonotic spillovers to sustained human-to-human transmission, disproportionately affecting vulnerable groups such as men-who-have-sex-with-men, immunocompromised individuals and marginalized populations with limited access to healthcare. This shift has been driven by critical mutations in genes associated with viral fitness, immune evasion and transmission dynamics. Moreover, these changes correspond with atypical and often milder yet more transmissible clinical presentations, complicating the detection and management of cases. Despite these challenges, health system preparedness has remained uneven. High-income countries leverage existing infrastructure to facilitate rapid responses through proactive policies and financial commitments. However, many low- and middle-income countries struggle with delayed case detection, limited surge capacity, community unawareness and fragmented outbreak governance. Although diagnostics, vaccines and antivirals have advanced, issues such as accessibility, affordability and distribution have persisted, hindering global solidarity efforts. This narrative review integrates evidence on the evolution of MPXV clades, clinical heterogeneity, and public health responses. Furthermore, by learning from past outbreaks, this review proposes actionable, time-sensitive recommendations to strengthen surveillance, ensure equitable deployment of countermeasures, secure supply chains and embed One Health approaches for increased resilience.

Jiao Pan, Tao Chen, Antonio Plaza

Revealing the spatial-temporal evolution and interactions of ecosystem services (ESs) in mining area is critical for sustainable environmental management. The temporal and spatial characteristics and changing trends of six ESs in Yuzhong mining area from 2000 to 2020 were analyzed. Pearson correlation analysis explored and elucidated the intricate tradeoffs and synergies that manifest across diverse ecosystems. The integrated ecosystem service landscape index (IESLI) was constructed on this basis, and 8 factors (both natural and human) were selected to identify the driving forces. The findings indicated that: 1) Over the past two decades, five categories of ESs have exhibited a declining trend, with water yield experiencing the most significant reduction, reaching 38.7% . 2) Among the 15 ESs pairings, tradeoffs were predominantly negatively correlated. 3) The interaction between land use/land cover and precipitation (54.5% ) emerged as the primary driving force behind the spatial heterogeneity of ESs. 4) The IESLI showed a general downward trend, decreasing from 0.51 in 2005 to 0.44 in 2020. This study provides quantitative evidence of ecosystem degradation and the intricate interrelationships among ESs in mining landscapes, highlighting the critical role of coupled spatial models in uncovering underlying patterns and mechanisms. The findings offer a scientific foundation for ecological restoration and policy-making in mining regions.

S. Almécija, Ashley S. Hammond, Nathan E. Thompson et al.

A distinctive ancestor There has been much focus on the evolution of primates and especially where and how humans diverged in this process. It has often been suggested that the last common ancestor between humans and other apes, especially our closest relative, the chimpanzee, was ape- or chimp-like. Almécija et al. review this area and conclude that the morphology of fossil apes was varied and that it is likely that the last shared ape ancestor had its own set of traits, different from those of modern humans and modern apes, both of which have been undergoing separate suites of selection pressures. Science, this issue p. eabb4363 A Review describes the unique and varied morphologies in fossil and modern apes, including humans. BACKGROUND Ever since the writings of Darwin and Huxley, humans’ place in nature relative to apes (nonhuman hominoids) and the geographic origins of the human lineage (hominins) have been heavily debated. Humans diverged from apes [specifically, the chimpanzee lineage (Pan)] at some point between ~9.3 million and ~6.5 million years ago (Ma), and habitual bipedalism evolved early in hominins (accompanied by enhanced manipulation and, later on, cognition). To understand the selective pressures surrounding hominin origins, it is necessary to reconstruct the morphology, behavior, and environment of the Pan-Homo last common ancestor (LCA). “Top-down” approaches have relied on living apes (especially chimpanzees) to reconstruct hominin origins. However, “bottom-up” perspectives from the fossil record suggest that modern hominoids represent a decimated and biased sample of a larger ancient radiation and present alternative possibilities for the morphology and geography of the Pan-Homo LCA. Reconciling these two views remains at the core of the human origins problem. ADVANCES There is no consensus on the phylogenetic positions of the diverse and widely distributed Miocene apes. Besides their fragmentary record, disagreements are due to the complexity of interpreting fossil morphologies that present mosaics of primitive and derived features, likely because of parallel evolution (i.e., homoplasy). This has led some authors to exclude known Miocene apes from the modern hominoid radiation. However, most researchers identify some fossil apes as either stem or crown members of the hominid clade [i.e., preceding the divergence between orangutans (pongines) and African great apes and humans (hominines), or as a part of the modern great ape radiation]. European Miocene apes have prominently figured in discussions about the geographic origin of hominines. “Kenyapith” apes dispersed from Africa into Eurasia ~16 to 14 Ma, and some of them likely gave rise to the European “dryopith” apes and the Asian pongines before 12.5 Ma. Some authors interpret dryopiths as stem hominines and support their back-to-Africa dispersal in the latest Miocene, subsequently evolving into modern African apes and hominins. Others interpret dryopiths as broadly ancestral to hominids or an evolutionary dead end. Increased habitat fragmentation during the late Miocene in Africa might explain the evolution of African ape knuckle walking and hominin bipedalism from an orthograde arboreal ancestor. Bipedalism might have allowed humans to escape the great ape “specialization trap“—an adaptive feedback loop between diet, specialized arboreal locomotion, cognition, and life history. However, understanding the different selection pressures that underlie knuckle walking and bipedalism is hindered by locomotor uncertainties about the Pan-Homo LCA and its Miocene forebears. In turn, the functional interpretation of Miocene ape mosaic morphologies is challenging because it depends on the relevance of primitive features. Furthermore, adaptive complexes can be co-opted to perform new functions during evolution. For instance, features that are functionally related to quadrupedalism or orthogrady can be misinterpreted as bipedal adaptations. Miocene apes show that the orthograde body plan, which predates below-branch suspension, is likely an adaptation for vertical climbing that was subsequently co-opted for other orthograde behaviors, including habitual bipedalism. OUTLOOK Future research efforts on hominin origins should focus on (i) fieldwork in unexplored areas where Miocene apes have yet to be found, (ii) methodological advances in morphology-based phylogenetics and paleoproteomics to retrieve molecular data beyond ancient DNA limits, and (iii) modeling driven by experimental data that integrates morphological and biomechanical information, to test locomotor inferences for extinct taxa. It is also imperative to stop assigning a starring role to each new fossil discovery to fit evolutionary scenarios that are not based on testable hypotheses. Early hominins likely originated in Africa from a Miocene LCA that does not match any living ape (e.g., it might not have been adapted specifically for suspension or knuckle walking). Despite phylogenetic uncertainties, fossil apes remain essential to reconstruct the “starting point” from which humans and chimpanzees evolved. The evolutionary history of apes and humans is largely incomplete. Whereas the phylogenetic relationships among living species can be retrieved using genetic data, the position of most extinct species remains contentious. Surprisingly, complete-enough fossils that can be attributed to the gorilla and chimpanzee lineages remain to be discovered. Assuming different positions of available fossil apes (or ignoring them owing to uncertainty) markedly affects reconstructions of key ancestral nodes, such as that of the chimpanzee-human LCA. Humans diverged from apes (chimpanzees, specifically) toward the end of the Miocene ~9.3 million to 6.5 million years ago. Understanding the origins of the human lineage (hominins) requires reconstructing the morphology, behavior, and environment of the chimpanzee-human last common ancestor. Modern hominoids (that is, humans and apes) share multiple features (for example, an orthograde body plan facilitating upright positional behaviors). However, the fossil record indicates that living hominoids constitute narrow representatives of an ancient radiation of more widely distributed, diverse species, none of which exhibit the entire suite of locomotor adaptations present in the extant relatives. Hence, some modern ape similarities might have evolved in parallel in response to similar selection pressures. Current evidence suggests that hominins originated in Africa from Miocene ape ancestors unlike any living species.

Carolien Bastiaanssen, Pilar Bobadilla Ugarte, Kijun Kim et al.

Abstract Argonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic Argonautes are subdivided into two clades: AGOs generally facilitate miRNA- or siRNA-mediated silencing, while PIWIs generally facilitate piRNA-mediated silencing. It is currently unclear when and how Argonaute-based RNA silencing mechanisms arose and diverged during the emergence and early evolution of eukaryotes. Here, we show that in Asgard archaea, the closest prokaryotic relatives of eukaryotes, an evolutionary expansion of Argonaute proteins took place. In particular, a deep-branching PIWI protein (HrAgo1) encoded by the genome of the Lokiarchaeon ‘Candidatus Harpocratesius repetitus’ shares a common origin with eukaryotic PIWI proteins. Contrasting known prokaryotic Argonautes that use single-stranded DNA as guides and/or targets, HrAgo1 mediates RNA-guided RNA cleavage, and facilitates gene silencing when expressed in human cells and supplied with miRNA precursors. A cryo-EM structure of HrAgo1, combined with quantitative single-molecule experiments, reveals that the protein displays structural features and target-binding modes that are a mix of those of eukaryotic AGO and PIWI proteins. Thus, this deep-branching archaeal PIWI may have retained an ancestral molecular architecture that preceded the functional and mechanistic divergence of eukaryotic AGOs and PIWIs.

Stuart A. MacGowan, Fábio Madeira, Thiago Britto-Borges et al.

Abstract Protein evolution is constrained by structure and function, creating patterns in residue conservation that are routinely exploited to predict structure and other features. Similar constraints should affect variation across individuals, but it is only with the growth of human population sequencing that this has been tested at scale. Now, human population constraint has established applications in pathogenicity prediction, but it has not yet been explored for structural inference. Here, we map 2.4 million population variants to 5885 protein families and quantify residue-level constraint with a new Missense Enrichment Score (MES). Analysis of 61,214 structures from the PDB spanning 3661 families shows that missense depleted sites are enriched in buried residues or those involved in small-molecule or protein binding. MES is complementary to evolutionary conservation and a combined analysis allows a new classification of residues according to a conservation plane. This approach finds functional residues that are evolutionarily diverse, which can be related to specificity, as well as family-wide conserved sites that are critical for folding or function. We also find a possible contrast between lethal and non-lethal pathogenic sites, and a surprising clinical variant hot spot at a subset of missense enriched positions.

Ganna Pletnyova

The article suggest to identify the principal types of descriptions of gender violence and their role in shaping the female characters of the historical novel «Man eaters» by the Ukrainian writer Zinaida Tulub, as well as to trace the influence of social and gender issues on the stylistic structure of the novel. Attention is drawn to the reflection of the theme of violence and its evolution in the history of Ukrainian literature. Attention is focused on the writer’s critical view of women’s fate in the Polish-Lithuanian Commonwealth, the Ottoman Empire, and the Tsardom of Muscovy of the 17th century. The following types of gender-based violence are systematized: rape, murder and abduction of children, human trafficking, everyday violence, religious control over women, etc. The author has recorded the main stylistic means used by Zinaida Tulub when depicting gender violence in the novel (landscapes, symbolic images, similes, etc.). The article offers a comparative analysis of two central female characters in the novel who are victims of these forms of gender violence: the Ukrainian peasant Horpyna Korzh, who finds herself in captivity in a Tatar village, and the Tatar peasant Medzhe, who is kidnapped by Ukrainian Cossacks. The parallel development of these female characters in the novel allows us to draw conclusions about the universality of this violence. An attempt is made to consider Zinaida Tulub’s works in the context of women’s prose in the 19th and at the beginning of the 20th centuries. Delving into the inner state of female characters experiencing deep emotional catastrophes is one of the characteristics of this prose. The appeal to the facts of the writer’s biography makes it possible to offer a feminist understanding of the work’s issues from the point of view of modern humanities. The article emphasizes the relevance of the study of gender violence in contemporary literary studies.

Mohammad Erfatpour, Dustin MacLean, Rachid Lahlali et al.

The ovule is a plant structure that upon fertilization, transforms into a seed. Successful fertilization is required for optimum crop productivity and is strongly affected by environmental conditions including temperature and precipitation. Climate change refers to sustained changes in global or regional climate patterns over an extended period, typically decades to millions of years. These shifts can result from natural processes like volcanic eruptions and solar radiation fluctuations, but in recent times, human activities—especially the burning of fossil fuels, deforestation, and industrial emissions—have accelerated the pace and scale of climate change. Human-induced climate change impacts the agricultural sector mainly through global warming and altering weather patterns, both of which create conditions that challenge agricultural production and food security. With food demand projected to sharply increase by 2050, urgent action is needed to prevent the worst impacts of climate change on food security and allow time for agricultural production systems to adapt and become more resilient. Gaining insights into the female reproductive part of the flower and seed development under extreme environmental conditions is important to oversee plant evolution, agricultural productivity, and food security in the face of climate change. This review summarizes the current knowledge on plant reproductive development and the effects of temperature and water stress, soil salinity, elevated carbon dioxide, and ozone pollution on the female reproductive structure and development across grain legumes, cereal, oilseed, and horticultural crops. It identifies gaps in existing studies for potential future research and suggests suitable mitigation strategies for sustaining crop productivity in a changing climate.

Ellinor O Alseth, Rafael Custodio, Sarah A Sundius et al.

Where there are bacteria, there will be bacteriophages. These viruses are known to be important players in shaping the wider microbial community in which they are embedded, with potential implications for human health. On the other hand, bacteria possess a range of distinct immune mechanisms that provide protection against bacteriophages, including the mutation or complete loss of the phage receptor, and CRISPR-Cas adaptive immunity. While our previous work showed how a microbial community may impact phage resistance evolution, little is known about the inverse, namely how interactions between phages and these different phage resistance mechanisms affect the wider microbial community in which they are embedded. Here, we conducted a 10-day, fully factorial evolution experiment to examine how phage impact the structure and dynamics of an artificial four-species bacterial community that includes either Pseudomonas aeruginosa wild-type or an isogenic mutant unable to evolve phage resistance through CRISPR-Cas. Additionally, we used mathematical modelling to explore the ecological interactions underlying full community behaviour, as well as to identify general principles governing the impacts of phage on community dynamics. Our results show that the microbial community structure is drastically altered by the addition of phage, with Acinetobacter baumannii becoming the dominant species and P. aeruginosa being driven nearly extinct, whereas P. aeruginosa outcompetes the other species in the absence of phage. Moreover, we find that a P. aeruginosa strain with the ability to evolve CRISPR-based resistance generally does better when in the presence of A. baumannii, but that this benefit is largely lost over time as phage is driven extinct. Finally, we show that pairwise data alone is insufficient when modelling our microbial community, both with and without phage, highlighting the importance of higher order interactions in governing multispecies dynamics in complex communities. Combined, our data clearly illustrate how phage targeting a dominant species allows for the competitive release of the strongest competitor while also contributing to community diversity maintenance and potentially preventing the reinvasion of the target species, and underline the importance of mapping community composition before therapeutically applying phage.

E. Hollox, L. Zuccherato, S. Tucci

Structural variation (SV) is a large difference (typically >100 bp) in the genomic structure of two genomes and includes both copy number variation and variation that does not change copy number of a genomic region, such as an inversion. Improved reference genomes, combined with widespread genome sequencing using short-read sequencing technology, and increasingly using long-read sequencing, have reignited interest in SV. Recent large-scale studies and functional focused analyses have highlighted the role of SV in human evolution. In this review, we highlight human-specific SVs involved in changes in the brain, population-specific SVs that affect response to the environment, including adaptation to diet and infectious diseases, and summarise the contribution of archaic hominin admixture to present-day human SV.

Alexis P. Sullivan, Douglas W. Bird, G. Perry

Jingmin An, Xiaogang Weng

Abstract Pre-trained natural language processing models on a large natural language corpus can naturally transfer learned knowledge to protein domains by fine-tuning specific in-domain tasks. However, few studies focused on enriching such protein language models by jointly learning protein properties from strongly-correlated protein tasks. Here we elaborately designed a multi-task learning (MTL) architecture, aiming to decipher implicit structural and evolutionary information from three sequence-level classification tasks for protein family, superfamily and fold. Considering the co-existing contextual relevance between human words and protein language, we employed BERT, pre-trained on a large natural language corpus, as our backbone to handle protein sequences. More importantly, the encoded knowledge obtained in the MTL stage can be well transferred to more fine-grained downstream tasks of TAPE. Experiments on structure- or evolution-related applications demonstrate that our approach outperforms many state-of-the-art Transformer-based protein models, especially in remote homology detection.

Vadim A. Maximov

Introduction. A. N. Radishchev in his writings lays the foundations of a humanistic study of Russian society and an anthropological understanding of economic orders. Most of the works were not published during his lifetime; the scientific publication of works and the study of views, mainly of a social nature, was undertaken in the 1940s–1950s. The comments emphasized the radical worldview of the thinker, manifested in the literary fi eld. In reality, the enlightener’s work is more multifaceted and covers philosophy, law, history, and economics. Three life periods are distinguished, diff erent in subject matter, but consonant with moral ideas. Theoretical analysis. The fi rst period of writing is characterized by works of social philosophy, fi ction and offi cial notes of a legal and economic nature, in which Radishchev’s ambivalent attitude to power, awmaking and moral values is revealed. The probable coincidence of the enlightener’s views with his European contemporaries (Locke, Diderot, A. Smith, Blackstone) and Russian philosophers (Tatishchev, Storkh) is revealed. Parallels with the works of I. Kant and the categorical apparatus of modern economic anthropology are determined. Empirical analysis. The views of Radishchev and Catherine II are interpreted in a comparative way. It is shown that there are no direct invectives in the “Journey from St. Petersburg to Moscow” against the Empress. The works on legislation in the third period of creativity are an adjusted continuation of the works of the fi rst period. The most complete economic and anthropological theme is presented in the essay “On Chinese Bargaining”, which implicitly rejects the principles of the government’s economic policy, which does not take into account the spatial identity of Russia, its civilizational mission and the potential of free enterprise. Results. The writings of A. N. Radishchev anticipate the fi eld of research of modern economic anthropology: the importance of refl ection in human behavior, its noumenal and phenomenal representation, historical construction of ways of action and thought, performative thinking, hierarchy and fragmentation of power, structuration of economic (market) relations are taken into consideration. The key concepts are collective faith, feelings and habits, inclinations and individual diff erences, good-action, objective and subjective interests, reasonableness and rationality in historical refraction. The problems of conciliarity, will, moral imperatives, acquisition of systematic knowledge, necessity of laws, human rights are highlighted as the most important from the position of the enlightener.

Daiki X. Sato, Yukiko U. Inoue, Nahoko Kuga et al.

Summary: The human vesicular monoamine transporter 1 (VMAT1) harbors unique substitutions (Asn136Thr/Ile) that affect monoamine uptake into synaptic vesicles. These substitutions are absent in all known mammals, suggesting their contributions to distinct aspects of human behavior modulated by monoaminergic transmissions, such as emotion and cognition. To directly test the impact of these human-specific mutations, we introduced the humanized residues into mouse Vmat1 via CRISPR/Cas9-mediated genome editing and examined changes at the behavioral, neurophysiological, and molecular levels. Behavioral tests revealed reduced anxiety-related traits of Vmat1Ile mice, consistent with human studies, and electrophysiological recordings showed altered oscillatory activity in the amygdala under anxiogenic conditions. Transcriptome analyses further identified changes in gene expressions in the amygdala involved in neurodevelopment and emotional regulation, which may corroborate the observed phenotypes. This knock-in mouse model hence provides compelling evidence that the mutations affecting monoaminergic signaling and amygdala circuits have contributed to the evolution of human socio-emotional behaviors.

Daniele Fundarò, Vito Gentile, Fabrizio Milazzo et al.

The evolution of computers in recent years has given a strong boost to research techniques aimed at improving human–machine interaction. These techniques tend to simulate the dynamics of the human–human interaction process, which is based on our innate ability to understand the emotions of other humans. In this work, we present the design of a classifier to recognize the emotions expressed by human beings, and we discuss the results of its testing in a culture-specific case study. The classifier relies exclusively on the gestures people perform, without the need to access additional information, such as facial expressions, the tone of a voice, or the words spoken. The specific purpose is to test whether a computer can correctly recognize emotions starting only from gestures. More generally, it is intended to allow interactive systems to be able to automatically change their behaviour based on the recognized mood, such as adapting the information contents proposed or the flow of interaction, in analogy to what normally happens in the interaction between humans. The document first introduces the operating context, giving an overview of the recognition of emotions and the approach used. Subsequently, the relevant bibliography is described and analysed, highlighting the strengths of the proposed solution. The document continues with a description of the design and implementation of the classifier and of the study we carried out to validate it. The paper ends with a discussion of the results and a short overview of possible implications.